Source code for weaver.processes.esgf_process

import re
import time
from collections import defaultdict
from typing import TYPE_CHECKING, Optional

import cwt  # noqa  # package: esgf-compute-api

from weaver.processes.wps1_process import Wps1Process
from weaver.status import Status
from weaver.utils import fetch_file

    from weaver.typedefs import JSON
    from typing import Dict, List, Tuple

[docs]LAST_PERCENT_REGEX = re.compile(r".+ (\d{1,3})$")
[docs]class Percent(object):
[docs] PREPARING = 2
[docs] SENDING = 3
[docs] COMPUTE_DONE = 98
[docs] FINISHED = 100
[docs]class InputNames(object):
[docs] FILES = "files"
[docs] VARIABLE = "variable"
[docs] API_KEY = "api_key"
[docs] TIME = "time"
[docs] LAT = "lat"
[docs] LON = "lon"
[docs]class InputArguments(object):
[docs] START = "start"
[docs] END = "end"
[docs] CRS = "crs"
[docs]class ESGFProcess(Wps1Process):
[docs] required_inputs = (InputNames.VARIABLE, )
[docs] def execute(self, workflow_inputs, out_dir, expected_outputs): # type: (JSON, str, Dict[str, str]) -> None """ Execute an ESGF process from cwl inputs. """ self._check_required_inputs(workflow_inputs) api_key = workflow_inputs.get(InputNames.API_KEY) inputs = self._prepare_inputs(workflow_inputs) domain = self._get_domain(workflow_inputs) esgf_process = self._run_process(api_key, inputs, domain) self._process_results(esgf_process, out_dir, expected_outputs)
[docs] def _prepare_inputs(self, workflow_inputs): # type: (JSON) -> List[cwt.Variable] """ Convert inputs from cwl inputs to ESGF format. """ message = "Preparing execute request for remote ESGF provider." self.update_status(message, Percent.PREPARING, Status.RUNNING) files = self._get_files_urls(workflow_inputs) varname = self._get_variable(workflow_inputs) inputs = [cwt.Variable(url, varname) for url in files] return inputs
[docs] def _get_domain(workflow_inputs): # type: (JSON) -> Optional[cwt.Domain] dimensions_names = [ InputNames.TIME, InputNames.LAT, InputNames.LON, ] grouped_inputs = defaultdict(dict) for dim_name in dimensions_names: for param, v in workflow_inputs.items(): if param.startswith(dim_name + "_"): param_split = param.split("_", 1)[1] grouped_inputs[dim_name][param_split] = v # grouped_inputs is of the form: # {"lat": {"start": 1, "end": 3, "crs": "values"}} # ensure data is casted properly for dim_name, values in grouped_inputs.items(): for value_name, value in values.items(): if value_name in [InputArguments.START, InputArguments.END] and value: values[value_name] = float(value) allowed_crs = { c for c in [cwt.VALUES, cwt.INDICES, cwt.TIMESTAMPS]} allowed_crs[None] = None # fix unintuitive latitude that must be given 'reversed' (start is larger than end) if InputNames.LAT in grouped_inputs: values = grouped_inputs[InputNames.LAT][InputArguments.START], \ grouped_inputs[InputNames.LAT][InputArguments.END] grouped_inputs[InputNames.LAT][InputArguments.START] = max(values) grouped_inputs[InputNames.LAT][InputArguments.END] = min(values) dimensions = [] for param_name, values in grouped_inputs.items(): for start_end in [InputArguments.START, InputArguments.END]: if start_end not in values: raise ValueError("Missing required parameter: {}_{}".format(param_name, start_end)) crs = cwt.VALUES if InputArguments.CRS in values: if values[InputArguments.CRS] not in allowed_crs: raise ValueError("CRS must be in {}".format(", ".join(map(str, allowed_crs)))) crs = allowed_crs[values[InputArguments.CRS]] dimension = cwt.Dimension(param_name, values[InputArguments.START], values[InputArguments.END], crs=crs) dimensions.append(dimension) if dimensions: domain = cwt.Domain( dimensions ) return domain
[docs] def _check_required_inputs(self, workflow_inputs): for required_input in self.required_inputs: if required_input not in workflow_inputs: raise ValueError("Missing required input: {}".format(required_input))
[docs] def _get_files_urls(workflow_inputs): # type: (JSON) -> List[Tuple[str, str]] """ Get all netcdf files from the cwl inputs. """ urls = [] files = workflow_inputs[InputNames.FILES] if not isinstance(files, list): files = [files] for cwl_file in files: if not cwl_file["class"] == "File": raise ValueError("'{}' inputs must have a class named 'File'".format(InputNames.FILES)) location = cwl_file["location"] if not location.startswith("http"): raise ValueError("ESGF processes only support urls for files inputs.") urls.append(location) return urls
[docs] def _get_variable(workflow_inputs): # type: (JSON) -> str """ Get all netcdf files from the cwl inputs. """ if InputNames.VARIABLE not in workflow_inputs: raise ValueError("Missing required input " + InputNames.VARIABLE) return workflow_inputs[InputNames.VARIABLE]
[docs] def _run_process(self, api_key, inputs, domain=None): # type: (str, List[cwt.Variable], Optional[cwt.Domain]) -> cwt.Process """ Run an ESGF process. """ wps = cwt.WPSClient(self.provider, api_key=api_key, verify=True) process = wps.processes(self.process)[0] message = "Sending request." self.update_status(message, Percent.SENDING, Status.RUNNING) wps.execute(process, inputs=inputs, domain=domain) self._wait(process) return process
[docs] def _wait(self, esgf_process, sleep_time=2): # type: (cwt.Process, float) -> bool """ Wait for an ESGF process to finish, while reporting its status. """ status_history = set() def update_history(): status = esgf_process.status status_percent = 0 # python 2 can't mutate nonlocal if status not in status_history: match = LAST_PERCENT_REGEX.match(status) if match: status_percent = int( status_percent = max(Percent.SENDING, status_percent) status_history.add(status) message = "ESGF status: " + status self.update_status(message, status_percent, Status.RUNNING) update_history() while esgf_process.processing: update_history() time.sleep(sleep_time) update_history() return esgf_process.succeeded
[docs] def _process_results(self, esgf_process, output_dir, expected_outputs): # type: (cwt.Process, str, Dict[str, str]) -> None """ Process the result of the execution. """ if not esgf_process.succeeded: message = "Process failed." self.update_status(message, Percent.FINISHED, Status.FAILED) return message = "Process successful." self.update_status(message, Percent.COMPUTE_DONE, Status.RUNNING) try: self._write_outputs(esgf_process.output.uri, output_dir, expected_outputs) except Exception: message = "Error while downloading files." self.update_status(message, Percent.FINISHED, Status.FAILED) raise
[docs] def _write_outputs(self, url, output_dir, expected_outputs): """ Write the output netcdf url to a local drive. """ message = "Downloading outputs." self.update_status(message, Percent.COMPUTE_DONE, Status.RUNNING) nc_outputs = [v for v in expected_outputs.values() if v.lower().endswith(".nc")] if len(nc_outputs) > 1: raise NotImplementedError("Multiple outputs are not implemented") fetch_file(url, output_dir, settings=self.settings) message = "Download successful." self.update_status(message, Percent.FINISHED, Status.SUCCEEDED)