def compute(self):
# Required input
in_dataset = self.getInputFromPort("in_dataset")
new_cons = set([Constraint('extra_info', ['nino34']),
Constraint('latsouth_info', ['5S']),
Constraint('latnorth_info', ['5N']),
Constraint('latagg_info', ['fldavg']),
Constraint('lonwest_info', ['190E']),
Constraint('loneast_info', ['240E']),
Constraint('lonagg_info', ['fldavg']),
Constraint('leveltop_info', ['surface']),
Constraint('levelbottom_info', ['surface']),
Constraint('anomaly_info', ['anom']),
])
# Execute the process.
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
new_cons,
positional_args=self.positional_args,
execution_options=self._execution_options)
try:
this_process.execute(simulate=configuration.simulate_execution)
except subprocess.CalledProcessError as e:
raise vistrails_module.ModuleError(self, e.output)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
# Required input
future_dataset = self.getInputFromPort("future_dataset")
baseline_dataset = self.getInputFromPort("baseline_dataset")
# Execute the process.
new_constraints = [Constraint('change_type', ['abs-change'])]
this_process = ProcessUnit(
[future_dataset, baseline_dataset],
self.out_pattern,
self.command,
extra_constraints=new_constraints,
execution_options=self._execution_options,
map_dict={
'fut_start': ('year_start', 0),
'fut_end': ('year_end', 0),
'hist_start': ('year_start', 1),
'hist_end': ('year_end', 1)
})
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, e.output)
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def submit(self, deps=True, noexec=False):
"""Submit the job to the queue.
@param deps: Whether or not to submit the tasks on which this task
depends.
@type deps: boolean
@param noexec: Whether or not to actually submit the job for execution.
If True the resulting shell script is printed to stdout.
@type noexec: boolean
"""
#Add directory creation
if len(self.outdirs) > 0:
self.add_pre_cmd(['mkdir', '-p'] + sorted(self.outdirs))
if noexec:
log.warning("Would run script:\n\n========>\n%s\n<========\n\n" % self.to_str())
else:
script_file, script_name = tempfile.mkstemp('.sh')
script_file = os.fdopen(script_file, 'w+b')
script_file.write(self.to_str() + '\n')
script_file.close()
args = ['sh', script_name]
#VERBOSE = os.getenv("VERBOSE")
#log.debug("SimpleJob.submit(): VERBOSE = '%s'" % VERBOSE)
try:
output = subprocess.check_output(args, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
output = e.output
raise vistrails_module.ModuleError(self, output) # we want the stderr
finally:
def compute(self):
in_dataset = self.getInputFromPort('in_dataset')
method = self.getInputFromPort('method')
self.positional_args = [(method, 0, 'raw'), ]
self.keyword_args = {}
if len(method.split(',')) > 1:
agg_constraint = "".join(method.split(','))
else:
agg_constraint = method
new_constraints_for_output = set([Constraint('timeagg_info', [agg_constraint]),
Constraint('suffix', ['nc']),
])
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
new_constraints_for_output,
execution_options=self._execution_options,
positional_args=self.positional_args,
cons_keywords=self.keyword_args)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
in_dataset1 = self.getInputFromPort('in_dataset1')
in_dataset2 = self.getInputFromPort('in_dataset2')
operation = self.getInputFromPort('operation')
self.positional_args = [
(operation, 0, 'raw'),
]
self.keyword_args = {}
new_constraints_for_output = set([
Constraint('extra_info', [operation]),
Constraint('suffix', ['nc']),
])
this_process = ProcessUnit([in_dataset1, in_dataset2],
self.out_pattern,
self.command,
new_constraints_for_output,
execution_options=self._execution_options,
positional_args=self.positional_args,
cons_keywords=self.keyword_args,
merge_output=['model', 'institute'])
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
# Required input
in_dataset = self.getInputFromPort("in_dataset")
# Set up the output command for this module, adding extra options.
positional_args = []
anom_label = 'anom-wrt-all'
arg_number = 0
try:
clim_bounds = self.getInputFromPort('clim_bounds')
positional_args += [('-b', arg_number, 'raw'),
(clim_bounds, arg_number + 1, 'raw')]
start_date, end_date = clim_bounds.split(',')
anom_label = 'anom-wrt-' + start_date + '-' + end_date
arg_number += 2
except vistrails_module.ModuleError as e:
pass
try:
timescale = self.getInputFromPort('timescale')
positional_args += [('-t', arg_number, 'raw'),
(timescale, arg_number + 1, 'raw')]
anom_label = timescale + anom_label
except vistrails_module.ModuleError as e:
pass
cons_for_output = set([
Constraint('suffix', ['nc']),
Constraint('anomaly_info', [anom_label])
])
# Execute the process.
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
cons_for_output,
positional_args=positional_args,
execution_options=self._execution_options)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
in_dataset = self.getInputFromPort('in_dataset')
# Change the file_type constraint from nc to xml
cons_for_output = set([Constraint('suffix', ['xml'])])
# Execute the cdscan
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
cons_for_output,
execution_options=self._execution_options)
try:
this_process.execute(simulate=configuration.simulate_execution)
except subprocess.CalledProcessError, e:
raise vistrails_module.ModuleError(self, e.output)
def compute(self):
in_dataset = self.getInputFromPort('in_dataset')
method = self.getInputFromPort('method')
seas_list = {'mon': 'ymon', 'seas': 'yseas', 'ann': 'tim'}
### loop over seas_list to generate all 3 season files ###
for seas in seas_list.keys():
self.positional_args = [
('%s%s' % (seas_list[seas], method), 0, 'raw'),
]
self.keyword_args = {}
if len(method.split(',')) > 1:
agg_constraint = "".join(method.split(','))
else:
agg_constraint = method
new_constraints_for_output = set([
Constraint(
'timeagg_info',
['%s%s' % (seas_list[seas], method)],
),
Constraint('suffix', ['nc']),
])
this_process = ProcessUnit(
[in_dataset],
self.out_pattern,
self.command,
new_constraints_for_output,
execution_options=self._execution_options,
positional_args=self.positional_args,
cons_keywords=self.keyword_args)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset_%s' % seas, process_output)
def compute(self):
in_dataset = self.getInputFromPort('in_dataset')
method = self.getInputFromPort('method')
grid = self.getInputFromPort('grid')
self.positional_args = [
(method, 0, 'raw'),
(grid, 1, 'raw'),
]
self.keyword_args = {}
grid = grid.split('/')[-1]
if len(grid.split('.')
) > 1: # i.e. a weights file as opposed to pre-defined grid
grid_constraint = method + '-' + grid.split('.')[0]
else:
grid_constraint = method + '-' + grid
new_constraints_for_output = set([
Constraint('grid_info', [grid_constraint]),
Constraint('suffix', ['nc']),
])
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
new_constraints_for_output,
execution_options=self._execution_options,
positional_args=self.positional_args,
cons_keywords=self.keyword_args)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
in_dataset1 = self.getInputFromPort('in_dataset1')
in_dataset2 = self.getInputFromPort('in_dataset2')
self.positional_args = []
self.keyword_args = {}
new_constraints_for_output = set([
Constraint('extra_info', ['timcor']),
Constraint('suffix', ['nc']),
])
merge_val = self.getInputFromPort('merge_constraints')
if merge_val:
extra_merge = [
cons_name.strip() for cons_name in merge_val.split(',')
]
else:
extra_merge = []
this_process = ProcessUnit([in_dataset1, in_dataset2],
self.out_pattern,
self.command,
new_constraints_for_output,
execution_options=self._execution_options,
positional_args=self.positional_args,
cons_keywords=self.keyword_args,
merge_output=extra_merge)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
# Required input
in_dataset = self.getInputFromPort("in_dataset")
# Set up the output command for this module, adding extra options.
positional_args = [('variable', 0)]
port_names = [
"timestart", "timeend", "lonwest", "loneast", "latsouth",
"latnorth", "levelbottom", "leveltop"
]
port_vals = {}
for name in port_names:
try:
port_vals[name + "_info"] = self.getInputFromPort(name)
except vistrails_module.ModuleError as e:
port_vals[name + "_info"] = None
arg_number = 3
cons_for_output = set([Constraint('suffix', ['nc'])])
if port_vals["timestart_info"] and port_vals["timeend_info"]:
positional_args += [('--time_bounds', arg_number, 'raw'),
('timestart_info', arg_number + 1),
('timeend_info', arg_number + 2)]
arg_number += 3
cons_for_output |= set([
Constraint('timestart_info', [port_vals["timestart_info"]]),
Constraint('timeend_info', [port_vals["timeend_info"]])
])
if port_vals["loneast_info"] and port_vals["lonwest_info"]:
positional_args += [('--lon_bounds', arg_number, 'raw'),
('lonwest_info', arg_number + 1),
('loneast_info', arg_number + 2)]
arg_number += 3
lonwest_text = longitude_label(port_vals["lonwest_info"])
loneast_text = longitude_label(port_vals["loneast_info"])
cons_for_output |= set([
Constraint('lonwest_info', [lonwest_text]),
Constraint('loneast_info', [loneast_text])
])
if port_vals["latsouth_info"] and port_vals["latnorth_info"]:
positional_args += [('--lat_bounds', arg_number, 'raw'),
('latsouth_info', arg_number + 1),
('latnorth_info', arg_number + 2)]
arg_number += 3
latsouth_text = latitude_label(port_vals["latsouth_info"])
latnorth_text = latitude_label(port_vals["latnorth_info"])
cons_for_output |= set([
Constraint('latsouth_info', [latsouth_text]),
Constraint('latnorth_info', [latnorth_text])
])
if port_vals["levelbottom_info"] and port_vals["leveltop_info"]:
positional_args += [('--level_bounds', arg_number, 'raw'),
('levelbottom_info', arg_number + 1),
('leveltop_info', arg_number + 2)]
arg_number += 3
cons_for_output |= set([
Constraint('levelbottom_info',
[port_vals["levelbottom_info"]]),
Constraint('leveltop_info', [port_vals["leveltop_info"]])
])
# Execute the xml_to_nc process.
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
cons_for_output,
positional_args=positional_args,
execution_options=self._execution_options)
try:
this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
process_output = this_process.file_creator
self.setResult('out_dataset', process_output)
def compute(self):
# Required input
in_dataset = self.getInputFromPort("in_dataset")
variable = self.getInputFromPort("variable")
#self.positional_args=[(variable_name, 0, 'raw')]
plot_type = self.getInputFromPort("plot_type")
#self.positional_args=[(plot_type, 1, 'raw')]
title = self.getInputFromPort("title")
#self.positional_args=[(title, 2, 'raw')]
region = self.getInputFromPort("region")
#self.positional_args=[(plot_type, 3, 'raw')]
colormap = self.getInputFromPort("colormap")
#self.positional_args=[(colormap, 4, 'raw')]
ticks = self.getInputFromPort("ticks")
#self.positional_args=[(plot_type, 5, 'raw')]
conv_units = self.getInputFromPort("conv_units")
#self.positional_args=[(conv_units, 6, 'raw')]
cons_for_output = set([Constraint('suffix', ['png'])])
run_opts = ''
if variable:
run_opts = run_opts + ' --variable %s' %variable
if plot_type:
run_opts = run_opts + ' --plot_type %s' %plot_type
if title:
run_opts = run_opts + ' --title %s' %title
if region:
run_opts = run_opts + ' --region %s' %region
if colormap:
run_opts = run_opts + ' --colourmap %s' %colormap
if ticks:
run_opts = run_opts + " --ticks '%s'" %ticks
if conv_units:
run_opts = run_opts + " --conv_units '%s'" %conv_units
# Execute plotting process.
this_process = ProcessUnit([in_dataset],
self.out_pattern,
self.command,
cons_for_output,
execution_options=self._execution_options,
#positional_args=self.positional_args,
kw_string=run_opts)
#kw_string="--title '${model}_${experiment}'")
try:
process_output = this_process.execute(simulate=configuration.simulate_execution)
except Exception as e:
raise vistrails_module.ModuleError(self, repr(e))
self.setResult('out_dataset', process_output)
