def _handler(self, request, response):
try:
wfdata = request.inputs["workflow"][0].data
LOGGER.debug(f"type wfdata={type(wfdata)}, wfdata={wfdata}")
# print(f"type wfdata={type(wfdata)}, wfdata={wfdata}")
# workaround for CDATA issue in pywps
# wfdata = wfdata.replace("<![CDATA[", "").replace("]]>", "")
wf = workflow.WorkflowRunner(output_dir=self.workdir)
file_uris = wf.run(wfdata)
except Exception as e:
raise ProcessError(f"{e}")
# Metalink document with collection of netcdf files
# ml4 = MetaLink4(
# "workflow-result", "Workflow result as NetCDF files.", workdir=self.workdir
# )
ml4 = build_metalink(
"workflow-result",
"Workflow result as NetCDF files.",
self.workdir,
file_uris,
)
# for ncfile in output:
# mf = MetaFile("NetCDF file", "NetCDF file", fmt=FORMATS.NETCDF)
# mf.file = ncfile
# ml4.append(mf)
response.outputs["output"].data = ml4.xml
response.outputs["prov"].file = wf.provenance.write_json()
response.outputs["prov_plot"].file = wf.provenance.write_png()
return response
def test_run_wf_cmip6_subset_average(tmp_path):
wfdoc = resource_file("wf_cmip6_subset_average.json")
wf = workflow.WorkflowRunner(output_dir=tmp_path)
output = wf.run(wfdoc)
assert (
"rlds_Amon_IPSL-CM6A-LR_historical_r1i1p1f1_gr_19850101-20140101_avg-year.nc"
in output[0])
def _handler(self, request, response):
wf = workflow.WorkflowRunner(
data_root_dir=configuration.get_config_value(
"data", "cmip5_archive_root"),
output_dir=self.workdir)
output = wf.run(request.inputs['workflow'][0].file)
response.outputs['output'].file = output[0]
return response
def test_wf_average_latlon_cmip6(tmp_path):
wfdoc = resource_file("wf_average_latlon_cmip6.json")
wf = workflow.WorkflowRunner(output_dir=tmp_path)
output = wf.run(wfdoc)
# print(output)
assert (
"rlds_Amon_IPSL-CM6A-LR_historical_r1i1p1f1_gr_19850116-20141216_avg-xy.nc"
in output[0])
def test_wf_c3s_cmip6_original_files(tmp_path):
wfdoc = resource_file("wf_c3s_cmip6_subset_original_files.json")
wf = workflow.WorkflowRunner(output_dir=tmp_path)
output = wf.run(wfdoc)
expected_url = (
"https://data.mips.copernicus-climate.eu/thredds/fileServer/esg_c3s-cmip6/"
"CMIP/SNU/SAM0-UNICON/historical/r1i1p1f1/day/pr/gn/v20190323/"
"pr_day_SAM0-UNICON_historical_r1i1p1f1_gn_18500101-18501231.nc")
assert expected_url in output
def _handler(self, request, response):
try:
wf = workflow.WorkflowRunner(output_dir=self.workdir)
output = wf.run(request.inputs['workflow'][0].file)
except Exception as e:
raise ProcessError(f"{e}")
# metalink document with collection of netcdf files
ml4 = MetaLink4('workflow-result',
'Workflow result as NetCDF files.',
workdir=self.workdir)
for ncfile in output:
mf = MetaFile('NetCDF file', 'NetCDF file', fmt=FORMATS.NETCDF)
mf.file = ncfile
ml4.append(mf)
response.outputs['output'].data = ml4.xml
return response
def test_workflow_runner_simple():
wf = workflow.WorkflowRunner(data_root_dir=CMIP5_ARCHIVE_ROOT,
output_dir=tempfile.mkdtemp())
output = wf.run(SIMPLE_WF)
assert 'output.nc' in output[0]
def test_run_tree_wf_5(tmp_path):
wf = workflow.WorkflowRunner(output_dir=tmp_path)
output = wf.run(TREE_WF_5)
assert (
"rlds_Amon_IPSL-CM6A-LR_historical_r1i1p1f1_gr_19950101-20000101_avg-year.nc"
in output[0])
def test_run_tree_wf_2(tmp_path):
wf = workflow.WorkflowRunner(output_dir=tmp_path)
output = wf.run(TREE_WF_2)
assert "tas_mon_HadGEM2-ES_rcp85_r1i1p1_20900101-21000101_avg-year.nc" in output[
0]
def test_workflow_runner_simple():
wf = workflow.WorkflowRunner(
output_dir=tempfile.mkdtemp())
output = wf.run(SIMPLE_WF)
assert 'tas_mon_HadGEM2-ES_rcp85_r1i1p1_20850116-21201216.nc' in output[0]