diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 9aa24c7..fa7118b 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -7,16 +7,15 @@ on: [push, pull_request] jobs: lint: runs-on: ubuntu-latest - env: - PYTHON: 3.9 + steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: lfs: 'true' - - name: Set up Python ${{ env.PYTHON }} - uses: actions/setup-python@v4 + - name: Set up Python 3.10 + uses: actions/setup-python@v5 with: - python-version: ${{ env.PYTHON }} + python-version: "3.10" - name: Python info run: | which python @@ -44,11 +43,11 @@ jobs: run: | sudo apt update sudo apt install libudunits2-dev - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: lfs: 'true' - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Python info diff --git a/setup.cfg b/setup.cfg index 8f6034d..14c9c27 100644 --- a/setup.cfg +++ b/setup.cfg @@ -43,10 +43,7 @@ test_require = tox:tox where=src [options.package_data] -* = - *.csv - *.toml - +* = *.csv, *.toml, *.json [options.entry_points] pyaro.timeseries = @@ -57,6 +54,7 @@ pyaro.timeseries = netcdf_rw = pyaro_readers.netcdf_rw:Netcdf_RWTimeseriesEngine harp = pyaro_readers.harpreader:AeronetHARPEngine nilupmfabsorption = pyaro_readers.nilupmfabsorptionreader:NILUPMFAbsorptionTimeseriesEngine + actrisebas = pyaro_readers.actrisebas:ActrisEbasTimeSeriesEngine nilupmfebas = pyaro_readers.nilupmfebas:EbasPmfTimeseriesEngine diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py new file mode 100644 index 0000000..6875085 --- /dev/null +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -0,0 +1,516 @@ +import datetime +import json +import logging +import os +import tomllib +from urllib.parse import urlparse, quote + +import numpy as np +import polars +import xarray as xr +from tqdm import tqdm +from urllib3.poolmanager import PoolManager +from urllib3.util.retry import Retry + +from pyaro.timeseries import ( + AutoFilterReaderEngine, + Data, + Flag, + NpStructuredData, + Station, +) + +logger = logging.getLogger(__name__) + +# default API URL base +BASE_API_URL = "https://dev-actris-md.nilu.no/" +# BASE_API_URL = "https://prod-actris-md.nilu.no/" +# base URL to query for data for a certain variable +VAR_QUERY_URL = f"{BASE_API_URL}metadata/content/" +# basename of definitions.toml which connects the pyaerocom variable names with the ACTRIS variable names +DEFINITION_FILE_BASENAME = "definitions.toml" +# online ressource of ebas flags +EBAS_FLAG_URL = "https://folk.nilu.no/~ebas/EBAS_Masterdata/ebas_flags.csv" + +DEFINITION_FILE = os.path.join( + os.path.dirname(os.path.realpath(__file__)), DEFINITION_FILE_BASENAME +) +# name of the standard_name section in the DEFINITION_FILE +STD_NAME_SECTION_NAME = "actris_standard_names" + +# number of times an api request is tried before we consider it failed +MAX_RETRIES = 2 + +# name of the root key containing the download information +DISTRIBUTION_ROOT_KEY = "md_distribution_information" +DISTRIBUTION_PROTOCOL_KEY = "protocol" +DISTRIBUTION_PROTOCOL_NAME = "OPeNDAP" +DISTRIBUTION_URL_KEY = "dataset_url" + +# some info to get to station name and location +LOCATION_ROOT_KEY = "md_data_identification" +LOCATION_FACILITY_KEY = "facility" +LOCATION_NAME_KEY = "name" +LOCATION_LAT_KEY = "lat" +LOCATION_LON_KEY = "lon" +LOCATION_ALT_KEY = "alt" + +# name of netcdf time variable in the netcdf files +# should be "time" as of CF convention, but other names can be added here +TIME_VAR_NAME = ["time"] + + +class ActrisEbasRetryException(Exception): + pass + + +class ActrisEbasStdNameNotFoundException(Exception): + pass + + +class ActrisEbasQcVariableNotFoundException(Exception): + pass + + +class ActrisEbasTestDataNotFoundException(Exception): + pass + + +class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): + def __init__( + self, + vars_to_read: list[str] = None, + filters=[], + tqdm_desc: str | None = None, + ts_type: str = "daily", + test_flag: bool = False, + ): + """ """ + self._filename = None + if isinstance(vars_to_read, str): + self.vars_to_read = [vars_to_read] + else: + self.vars_to_read = vars_to_read + self._stations = {} + self.urls_to_dl = {} + self._data = {} # var -> {data-array} + self._set_filters(filters) + # self._header = [] + self._metadata = {} + # used for variable matching in the EBAS data files + # gives a mapping between the EBAS or pyaerocom variable name + # and the CF standard name found in the EBAS data files + # Due to standard_names aliases, the values are a list + self.standard_names = {} + # _laststatstr = "" + self._revision = datetime.datetime.now() + self._metadata["revision"] = datetime.datetime.strftime( + self._revision, "%y%m%d%H%M%S" + ) + self.ebas_flags = self.get_ebas_flags() + + # if "variables" in filters: + # if "include" in filters["variables"]: + # self.vars_to_read = filters["variables"]["include"] + # logger.info(f"applying variable include filter {vars_to_read}...") + + # read only stations according to the station filter + try: + self.sites_to_read = filters["stations"]["include"] + except (KeyError, TypeError) as e: + self.sites_to_read = [] + + try: + self.sites_to_exclude = filters["stations"]["exclude"] + except (KeyError, TypeError) as e: + self.sites_to_exclude = [] + + # since the current pyaerocom interface limits vars_to_read to a string + # (and foresees the variables to be passed via a filter) just overwrite + # vars_to_read with the settings from the filter if a variable filter has been supplied + if "variables" in filters: + try: + self.vars_to_read = filters["variables"]["include"] + logger.info(f"applying variable include filter {vars_to_read}...") + except (KeyError, TypeError) as e: + pass + + # read config file + self.def_data = self._read_definitions(file=DEFINITION_FILE) + # Because the user might have given a pyaerocom name, build self.actris_vars_to_read with a list + # of ACTRIS variables to read. values are a list + self.actris_vars_to_read = {} + for var in self.vars_to_read: + self._metadata[var] = {} + # handle pyaerocom variables here: + # if a given variable name is in the list of pyaerocom variable names in definitions.toml + self.actris_vars_to_read[var] = [] + if var in self.def_data["variables"]: + # user gave a pyaerocom variable name + self.actris_vars_to_read[var] = self.def_data["variables"][var][ + "actris_variable" + ] + for _actris_var in self.actris_vars_to_read[var]: + try: + self.standard_names[var].extend( + self.get_actris_standard_name(_actris_var) + ) + self.standard_names[_actris_var].extend( + self.get_actris_standard_name(_actris_var) + ) + except KeyError: + self.standard_names[var] = self.get_actris_standard_name( + _actris_var + ) + self.standard_names[ + _actris_var + ] = self.get_actris_standard_name(_actris_var) + + else: + # user gave ACTRIS name + self.actris_vars_to_read[var].append(var) + self.standard_names[var] = self.get_actris_standard_name(var) + + for _pyaro_var in self.actris_vars_to_read: + self._metadata[_pyaro_var] = {} + for _actris_var in self.actris_vars_to_read[_pyaro_var]: + # for testing since the API is error-prone and slow at the time of this writing + test_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + f"{_actris_var}.json", + ) + if os.path.exists(test_file) and test_flag: + with open(test_file, "r") as f: + json_resp = json.load(f) + else: + page_no = 0 + json_resp_tmp = "bla" + json_resp = [] + while len(json_resp_tmp) != 0: + # search for variable metadata + query_url = f"{VAR_QUERY_URL}{quote(self.actris_vars_to_read[_pyaro_var][0])}/page/{page_no}" + logger.info(query_url) + retries = Retry(connect=5, read=2, redirect=5) + http = PoolManager(retries=retries) + response = http.request("GET", query_url) + if len(response.data) > 0: + try: + json_resp_tmp = json.loads( + response.data.decode("utf-8") + ) + except json.decoder.JSONDecodeError: + json_resp_tmp = json.loads(response.data) + + json_resp.extend(json_resp_tmp) + page_no += 1 + else: + json_resp_tmp = "" + continue + + self._metadata[_pyaro_var][_actris_var] = json_resp + self.urls_to_dl[_actris_var] = self.extract_urls( + json_resp, + sites_to_read=self.sites_to_read, + sites_to_exclude=self.sites_to_exclude, + ) + # The following needs some refinement once we read pyaerocom variables that hold more than + # one EBAS variable + # we need to decide per station which EBAS variable to return at a certain station and potentially time + # self.read_data( + # actris_variable=_pyaro_var, urls_to_dl=self.urls_to_dl[_actris_var] + # ) + # assert self._data[_pyaro_var] + # return _pyaro_var, self.urls_to_dl + + def metadata(self): + return self._metadata + + def read( + self, + tqdm_desc="reading stations", + ): + """ + read the data from EBAS thredds server + """ + # for actris vocabulary key and value of self.actris_vars_to_read are the same + # for pyaerocom vocabulary they are not (key is pyaerocom variable name there)! + for _var in self.actris_vars_to_read: + if _var in self._data: + logger.info(f"var {_var} already read") + continue + for actris_variable in self.actris_vars_to_read[_var]: + # actris_variable = self.actris_vars_to_read[_var][0] + + urls_to_dl = self.urls_to_dl[actris_variable] + bar = tqdm(desc=tqdm_desc, total=len(urls_to_dl), disable=None) + for s_idx, site_name in enumerate(urls_to_dl): + for f_idx, url in enumerate(urls_to_dl[site_name]): + logger.info(f"reading file {url}") + tmp_data = xr.open_dataset(url) + + # put all data variables in the data struct for the moment + for d_idx, _data_var in enumerate( + self._get_ebas_data_vars( + tmp_data, + ) + ): + # look for a standard_name match and return only that variable + std_name = self.get_ebas_data_standard_name( + tmp_data, _data_var + ) + if std_name not in self.standard_names[actris_variable]: + # logger.info( + # f"station {site_name}, file #{f_idx}: skipping variable {_data_var} due to wrong standard name" + # ) + continue + else: + log_str = f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" + logger.info(log_str) + + # assert f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" + long_name = tmp_data.attrs["ebas_station_name"] + stat_code = tmp_data.attrs["ebas_station_code"] + # create variables valid for all measured variables... + start_time = np.asarray(tmp_data["time_bnds"][:, 0]) + stop_time = np.asarray(tmp_data["time_bnds"][:, 1]) + ts_no = len(start_time) + lat = np.full(ts_no, tmp_data.attrs["geospatial_lat_min"]) + lon = np.full(ts_no, tmp_data.attrs["geospatial_lon_min"]) + # station = np.full(ts_no, tmp_data.attrs["ebas_station_code"]) + station = np.full(ts_no, long_name) + altitude = np.full( + ts_no, tmp_data.attrs["geospatial_vertical_min"] + ) + standard_deviation = np.full(ts_no, np.nan) + vals = tmp_data[_data_var].values + # apply flags + ebas_qc_var = self.get_ebas_data_qc_variable( + tmp_data, _data_var + ) + + flags = np.full(ts_no, Flag.VALID) + if _var not in self._data: + self._data[_var] = NpStructuredData( + _var, + self.get_ebas_data_units(tmp_data, _data_var), + ) + + self._data[_var].append( + value=vals, + station=station, + latitude=lat, + longitude=lon, + altitude=altitude, + start_time=start_time, + end_time=stop_time, + # TODO: Currently assuming that all observations are valid. + flag=flags, + standard_deviation=standard_deviation, + ) + # stop after the 1st matching variable + logger.info( + f"matching std_name found. Not searching for possible additional std_name matches at this point..." + ) + break + + if not site_name in self._stations: + self._stations[site_name] = Station( + { + "station": stat_code, + "longitude": lon[0], + "latitude": lat[0], + "altitude": altitude[0], + "country": self.get_ebas_data_country_code(tmp_data), + "url": "", + # This is used by pyaerocom + "long_name": site_name, + } + ) + bar.update(1) + bar.close() + assert True + + def get_ebas_flags(self, url: str = EBAS_FLAG_URL) -> dict: + """small helper to download the bas flag file from NILU""" + + df = polars.read_csv(url) + # return this as a python dict for now + ret_data = {} + for var in df.columns: + ret_data[var] = df[var].to_numpy() + + # for simplicity add a dict entry listing the valid flags + # last column is the explanation ("V" for valid) + ret_data["valid"] = ret_data["Flag"][var == "V"] + + return ret_data + + # decoded_content = download.content.decode('utf-8') + def get_ebas_data_units(self, tmp_data, var_name): + """small helper method to get the ebas unit from the data file""" + unit = tmp_data[var_name].attrs["units"] + return unit + + def get_ebas_data_standard_name(self, tmp_data, var_name): + """small helper method to get the ebas standard_name for a given variable from the data file""" + ret_data = "" + try: + ret_data = tmp_data[var_name].attrs["standard_name"] + except KeyError: + pass + return ret_data + + def get_ebas_data_ancillary_variables(self, tmp_data, var_name): + """ + small helper method to get the ebas ancillary variables from the data file + These contain the data flags (hopefully always ending with "_qc" and additional metedata + (hopefully always ending with "_ebasmetadata" for each time step + """ + ret_data = tmp_data[var_name].attrs["ancillary_variables"].split() + return ret_data + + def get_ebas_data_qc_variable(self, tmp_data, var_name): + """ + small helper method to get the ebas quality control variable name + for a given variable name in the ebas data file + uses self.get_ebas_data_ancillary_variables to get the variable names of the + ancillary variables + """ + ret_data = None + for var in self.get_ebas_data_ancillary_variables(tmp_data, var_name): + for time_name in TIME_VAR_NAME: + if time_name in tmp_data[var_name].dims: + return var + if ret_data is None: + raise ActrisEbasQcVariableNotFoundException( + f"Error: no flag data for variable {var_name} found!" + ) + return "" + + def get_ebas_data_country_code(self, tmp_data): + """small helper method to get the ebas country code from the data file""" + return tmp_data.attrs["ebas_station_code"][0:2] + + def get_actris_standard_name(self, actris_var_name): + """small helper method to get corresponding CF standard name for a given ACTRIS variable""" + try: + return self.def_data[STD_NAME_SECTION_NAME][actris_var_name] + except KeyError: + raise ActrisEbasStdNameNotFoundException( + f"Error: no CF standard name for {actris_var_name} found!" + ) + + def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = None): + """ + small helper method to isolate potential data variables + since the variable names have no meaning (even if it seems otherwise) + + Selects potential data variables based on which dimension they depend on + Data variables depend on the time dimension only + """ + + data_vars = [] + for data_var in tmp_data.data_vars: + if len(tmp_data[data_var].dims) != 1: + continue + elif tmp_data[data_var].dims[0] in TIME_VAR_NAME: + # check for standard unit + try: + # if defined, return only names that match + if ( + tmp_data[data_var].attrs["units"] + == self.def_data["actris_std_units"][data_var] + ): + data_vars.append(data_var) + except KeyError: + data_vars.append(data_var) + + return data_vars + + def extract_urls( + self, + json_resp: dict, + sites_to_read: list[str] = [], + sites_to_exclude: list[str] = [], + ) -> dict: + """ + small helper method to extract URLs to download from json reponse from the EBAS API + """ + urls_to_dl = {} + # highest hierachy is a list + for site_idx, site_data in enumerate(json_resp): + site_name = site_data[LOCATION_ROOT_KEY][LOCATION_FACILITY_KEY][ + LOCATION_NAME_KEY + ] + if site_name in sites_to_exclude: + logger.info(f"site {site_name} excluded due to exclusion filter") + continue + if site_name in sites_to_read or len(sites_to_read) == 0: + if site_name not in urls_to_dl: + urls_to_dl[site_name] = [] + + # site_data[DISTRIBUTION_ROOT_KEY] is also a list + # search for protocol DISTRIBUTION_PROTOCOL_NAME + for url_idx, distribution_data in enumerate( + site_data[DISTRIBUTION_ROOT_KEY] + ): + if ( + distribution_data[DISTRIBUTION_PROTOCOL_KEY] + != DISTRIBUTION_PROTOCOL_NAME + ): + logger.info( + f"skipping site: {site_name} / proto: {distribution_data[DISTRIBUTION_PROTOCOL_KEY]}" + ) + continue + else: + urls_to_dl[site_name].append( + distribution_data[DISTRIBUTION_URL_KEY] + ) + logger.info( + f"site: {site_name} / proto: {distribution_data[DISTRIBUTION_PROTOCOL_KEY]} included in URL list" + ) + break + return urls_to_dl + + def _unfiltered_data(self, varname) -> Data: + self.read() + return self._data[varname] + + def _unfiltered_stations(self) -> dict[str, Station]: + self.read() + return self._stations + + def _unfiltered_variables(self) -> list[str]: + self.read() + return list(self._data.keys()) + + def close(self): + pass + + def _read_definitions(self, file=DEFINITION_FILE): + # definitions file for a connection between aerocom names, ACTRIS vocabulary and EBAS vocabulary + # The EBAS part will hopefully not be necessary in the next EBAS version anymore + with open(file, "rb") as fh: + tmp = tomllib.load(fh) + return tmp + + def is_valid_url(self, url): + try: + result = urlparse(url) + return all([result.scheme, result.netloc]) + except ValueError: + return False + + +class ActrisEbasTimeSeriesEngine(AutoFilterReaderEngine.AutoFilterEngine): + def reader_class(self): + return ActrisEbasTimeSeriesReader + + def open(self, *args, **kwargs) -> ActrisEbasTimeSeriesReader: + return self.reader_class()(*args, **kwargs) + + def description(self): + return "ACTRIS EBAS reader using the pyaro infrastructure" + + def url(self): + return "https://github.com/metno/pyaro-readers" diff --git a/src/pyaro_readers/actrisebas/__init__.py b/src/pyaro_readers/actrisebas/__init__.py new file mode 100644 index 0000000..e29df4d --- /dev/null +++ b/src/pyaro_readers/actrisebas/__init__.py @@ -0,0 +1,4 @@ +from .ActrisEbasReader import ( + ActrisEbasTimeSeriesReader, + ActrisEbasTimeSeriesEngine, +) diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml new file mode 100644 index 0000000..0731e44 --- /dev/null +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -0,0 +1,85 @@ +# connection between pyaerocom and ACTRIS-EBAS variables +[variables] +#prototype +# the order in the list below is preserved and determines the order the data is read +#[variables.] +#actris_variable = [] +#actris_matrix = [] +#ebas_component = [] +#ebas_matrix = [] + +[variables.conco3] +actris_variable = ["ozone mass concentration"] +actris_matrix = ["gas phase"] +ebas_component = ["ozone"] +ebas_matrix = ["air"] +standard_names = ["mass_concentration_of_ozone_in_air"] + +[variables.vmro3] +#actris_variable = ["ozone amount fraction"] +actris_variable = ["ozone mass concentration"] +actris_matrix = ["gas phase"] +ebas_component = ["ozone"] +ebas_matrix = ["air"] +standard_names = ["mole_fraction_of_ozone_in_air"] + + +[variables.concso4t] +actris_variable = ["aerosol particle sulphate mass concentration"] +actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] +ebas_component = ["sulphate_total"] +ebas_matrix = ["aerosol", "pm10", "pm25"] +standard_names = ["mass_concentration_of_total_sulphateexpressed_as_sulphur_in_dry_aerosol_particles_in_air", + "mass_concentration_of_sulphate_total_in_pm10_in_air", + "mass_concentration_of_sulphate_total_in_pm2p5_in_air", ] + +[variables.concso4c] +actris_variable = ["aerosol particle sulphate mass concentration"] +actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] +ebas_component = ["sulphate_corrected"] +ebas_matrix = ["aerosol", "pm10", "pm25"] +standard_names = ["mass_concentration_of_sulphate_corrected_for_seaspray_expressed_as_sulphur_in_dry_aerosol_particles_in_air", + "mass_concentration_of_sulphate_corrected_for_seaspray_expressed_as_sulphur_in_pm10_in_air", + "mass_concentration_of_sulphate_corrected_for_seaspray_expressed_as_sulphur_in_pm2p5_in_air", ] + +[variables.concCecpm25] +actris_variable = ["aerosol particle elemental carbon mass concentration"] +actris_matrix = ["aerosol particle phase"] +ebas_component = ["elemental_carbon"] +ebas_matrix = ["pm25", "pm1"] +standard_names = ["mass_concentration_of_elemental_carbon_in_pm2p5_in_air", + "mass_concentration_of_elemental_carbon_in_pm1_in_air", ] + +[variables.concCsopm25] +actris_variable = ["aerosol particle organic carbon mass concentration"] +actris_matrix = ["aerosol particle phase"] +ebas_component = ["organic_carbon"] +ebas_matrix = ["pm25", "pm1"] +standard_names = ["mass_concentration_of_organic_carbon_in_pm2p5_in_air", + "mass_concentration_of_organic_carbon_in_pm1_in_air", ] + +#[actris_std_units] +# tell the reader which unit shall be returned in case the same property is available in several units +# e.g. ozone mass concentration is available in the files in [ug/m3] and [nmol/mol] +# make sure to use ACTRIS-EBAS unit notation since this is a simple string match +# For variables not noted here, we will return the first unit found in the first data file +#"ozone mass concentration" = "ug/m3" +#"ozone amount fraction" = "nmol/mol" +#"aerosol particle sulphate mass concentration" = "ug/m3" + +[actris_standard_names] +# match between ACTRIS vocabulary and CF standard name +# needed to match the variables in multicolumn files since the netcdf variable name has no meaning +# the standard_names are not unique for a given ACTRIS species, therefore a list +"ozone mass concentration" = ["mass_concentration_of_ozone_in_air"] +"ozone amount fraction" = ["mole_fraction_of_ozone_in_air"] +"aerosol particle sulphate mass concentration" = ["mass_concentration_of_total_sulphateexpressed_as_sulphur_in_dry_aerosol_particles_in_air", + "mass_concentration_of_sulphate_total_in_pm10_in_air", + "mass_concentration_of_sulphate_total_in_pm2p5_in_air", ] +#"" = "mass_concentration_of_sulphate_corrected_for_seaspray_expressed_as_sulphur_in_dry_aerosol_particles_in_air" +#"" = "" +#"" = "" +"aerosol particle elemental carbon mass concentration" = ["mass_concentration_of_elemental_carbon_in_pm2p5_in_air", + "mass_concentration_of_elemental_carbon_in_pm1_in_air", ] +"aerosol particle organic carbon mass concentration" = ["mass_concentration_of_organic_carbon_in_pm2p5_in_air", + "mass_concentration_of_organic_carbon_in_pm1_in_air", ] diff --git a/src/pyaro_readers/actrisebas/ozone mass concentration.json b/src/pyaro_readers/actrisebas/ozone mass concentration.json new file mode 100644 index 0000000..1b286b7 --- /dev/null +++ b/src/pyaro_readers/actrisebas/ozone mass concentration.json @@ -0,0 +1,83768 @@ +[ + { + "md_metadata": { + "id": 203110, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "RTXS-U8P8.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-13T22:00:00.0000000Z", + "created": "2024-06-14T08:00:07.0000000Z", + "contact": [ + { + "first_name": "Markus", + "last_name": "Fiebig", + "organisation_name": "NILU", + "role_code": [ + "custodian" + ], + "country_code": "NO", + "delivery_point": "Instituttveien 18", + "address_city": "Kjeller", + "administrative_area": "Viken", + "postal_code": 2007, + "email": "ebas@nilu.no", + "position_name": "Senior Scientist" + } + ] + }, + "md_identification": { + "abstract": "Ozone at Arkona. 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These measurements are gathered as a part of the following projects GAW-WDCRG", + "title": "Ozone at Yonaguni", + "date_type": "creation", + "contact": [ + { + "first_name": "Yong", + "last_name": "Lin", + "organisation_name": "NILU", + "role_code": [ + "pointOfContact" + ], + "country_code": "NO", + "email": "ebas@nilu.no" + } + ], + "online_resource": { + "linkage": "https://ebas-data.nilu.no/" + }, + "identifier": { + "pid": "https://doi.org/10.48597/EK83-VS9N", + "type": "DOI" + }, + "date": "2024-06-14T22:00:00.0000000Z" + }, + "md_constraints": { + "access_constraints": "license", + "use_constraints": "license", + "other_constraints": "N/A", + "data_licence": "CC-BY-4.0", + "metadata_licence": "CC-BY-4.0", + "citation": "Takizawa, A., Ueno, M., Saito, K., Sawa, Y., Shinya, T., Tsuboi, K., GAW-WDCRG, 2007-2024, Ozone at Yonaguni, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/EK83-VS9N", + "acknowledgement": "Data used in this were accessed from EBAS \n (https://ebas.nilu.no) hosted by NILU.\nSpecifically, the use included data affiliated with the framework: GAW-WDCRG." + }, + "md_keywords": { + "keywords": [ + "atmosphere", + "gas phase", + "gaw-wdcrg", + "ozone mass concentration", + "ultra-violet fluorescence detector" + ] + }, + "md_data_identification": { + "language": "en", + "topic_category": "climatologyMeteorologyAtmosphere", + "description": "time series of point measurements at surface", + "facility": { + "identifier": "zwqq", + "name": "Yonaguni", + "lat": 24.466941, + "lon": 123.010872, + "alt": 30.0, + "country_code": "JP", + "wmo_region": "Asia", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/zwqq" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 123.010872, + "east_bound_longitude": 123.010872, + "south_bound_latitude": 24.466941, + "north_bound_latitude": 24.466941 + }, + "ex_temporal_extent": { + "time_period_begin": "2007-12-30T23:00:00.0000000Z", + "time_period_end": "2024-01-30T23:00:00.0000000Z" + }, + "ex_vertical_extent": null, + "md_content_information": { + "attribute_descriptions": [ + "ozone mass concentration" + ], + "content_type": "physicalMeasurement" + }, + "md_distribution_information": [ + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/dodsC/ebas_doi/EK/83/VS/EK83-VS9N.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 5775490.0 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/EK/83/VS/EK83-VS9N.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 5775490.0 + } + ], + "md_actris_specific": { + "facility_type": "observation platform, fixed", + "product_type": "observation", + "matrix": "gas phase", + "sub_matrix": null, + "instrument_type": [ + "ultra-violet fluorescence detector" + ], + "program_affiliation": [ + "GAW-WDCRG" + ], + "variable_statistical_property": null, + "legacy_data": true, + "observation_timeliness": "scheduled", + "data_product": "full quality control", + "instrument_model": "Thermo/49i" + }, + "dq_data_quality_information": { + "compliance": "ACTRIS associated" + }, + "provenance": { + "software": "https://git.nilu.no/ebas/ebas-io", + "version_history": null + } + } +] \ No newline at end of file diff --git a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py index baa2da5..425cf3d 100644 --- a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py @@ -5,6 +5,7 @@ from urllib.parse import urlparse from urllib.request import urlopen from zipfile import BadZipFile, ZipFile + import datetime import numpy as np @@ -101,10 +102,17 @@ def __init__( self._data = {} # var -> {data-array} self._set_filters(filters) self._header = [] - _laststatstr = "" self._revision = datetime.datetime.min + self.fill_country_flag = fill_country_flag + self.ts_type = ts_type + self.tqdm_desc = tqdm_desc + def read(self): # check if file is a URL + _laststatstr = "" + # check if the data has been read already + if len(self._data) != 0: + return if self.is_valid_url(self._filename): # try to open as zipfile try: @@ -175,7 +183,7 @@ def __init__( gcd = Geocoder_Reverse_NE() crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) - bar = tqdm(desc=tqdm_desc, total=len(lines), disable=None) + bar = tqdm(desc=self.tqdm_desc, total=len(lines), disable=None) for _ridx, row in enumerate(crd): bar.update(1) if row[SITE_NAME] != _laststatstr: @@ -185,7 +193,7 @@ def __init__( lon = float(row[LON_NAME]) lat = float(row[LAT_NAME]) alt = float(row["Site_Elevation(m)"]) - if fill_country_flag: + if self.fill_country_flag: try: country = gcd.lookup(lat, lon)["ISO_A2_EH"] except Geocoder_Reverse_Exception: @@ -230,8 +238,8 @@ def __init__( ] ) time_dummy = np.datetime64(datestring) - start = time_dummy - TS_TYPE_DIFFS[ts_type] - end = time_dummy + TS_TYPE_DIFFS[ts_type] + start = time_dummy - TS_TYPE_DIFFS[self.ts_type] + end = time_dummy + TS_TYPE_DIFFS[self.ts_type] ts_dummy_data = {} for variable in DATA_VARS: @@ -271,15 +279,19 @@ def __init__( bar.close() def metadata(self): + self.read() return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) def _unfiltered_data(self, varname) -> Data: + self.read() return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: + self.read() return self._stations def _unfiltered_variables(self) -> list[str]: + self.read() return list(self._data.keys()) def close(self): diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 12a9f73..b7a8525 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,15 +1,18 @@ import csv +import datetime from io import BytesIO from urllib.parse import urlparse from urllib.request import urlopen from zipfile import BadZipFile, ZipFile +import numpy as np +import requests from geocoder_reverse_natural_earth import ( Geocoder_Reverse_NE, Geocoder_Reverse_Exception, ) -import numpy as np -import requests +from tqdm import tqdm + from pyaro.timeseries import ( AutoFilterReaderEngine, Data, @@ -17,8 +20,6 @@ NpStructuredData, Station, ) -from tqdm import tqdm -import datetime # default URL BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" @@ -47,7 +48,7 @@ # The computed variables have to be named after the read ones, otherwise the calculation will fail! DATA_VARS.extend(COMPUTED_VARS) -FILL_COUNTRY_FLAG = False +FILL_COUNTRY_FLAG = True TS_TYPE_DIFFS = { "daily": np.timedelta64(12, "h"), @@ -90,9 +91,20 @@ def __init__( self._data = {} # var -> {data-array} self._set_filters(filters) self._header = [] - _laststatstr = "" + self._revision = datetime.datetime.min + self.fill_country_flag = fill_country_flag + self.ts_type = ts_type + + def read( + self, + tqdm_desc="reading stations", + ): # check if file is a URL + _laststatstr = "" + # check if the data has been read already + if len(self._data) != 0: + return if self.is_valid_url(self._filename): # try to open as zipfile try: @@ -128,7 +140,7 @@ def __init__( lon = float(row[LON_NAME]) lat = float(row[LAT_NAME]) alt = float(row["Site_Elevation(m)"]) - if fill_country_flag: + if self.fill_country_flag: try: country = gcd.lookup(lat, lon)["ISO_A2_EH"] except Geocoder_Reverse_Exception: @@ -173,8 +185,8 @@ def __init__( ] ) time_dummy = np.datetime64(datestring) - start = time_dummy - TS_TYPE_DIFFS[ts_type] - end = time_dummy + TS_TYPE_DIFFS[ts_type] + start = time_dummy - TS_TYPE_DIFFS[self.ts_type] + end = time_dummy + TS_TYPE_DIFFS[self.ts_type] ts_dummy_data = {} for variable in DATA_VARS: @@ -200,15 +212,19 @@ def __init__( bar.close() def metadata(self): + self.read() return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) def _unfiltered_data(self, varname) -> Data: + self.read() return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: + self.read() return self._stations def _unfiltered_variables(self) -> list[str]: + self.read() return list(self._data.keys()) def close(self): diff --git a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py index 1c4d1af..59a749c 100644 --- a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py +++ b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py @@ -49,6 +49,7 @@ def __init__( :param filters: list of filters, defaults to [] """ self._set_filters(filters) + self._revision = datetime.datetime.now() if os.path.isdir(filename): self._directory = filename else: @@ -70,6 +71,9 @@ def __init__( if self._is_year_in_filters(year): self._years.add(year) + self._metadata = self.metadata() + + # def read(self): self._variables = self._read_file_variables() station_file = "StationList.csv" station_filepath = os.path.join(self._directory, station_file) @@ -79,7 +83,7 @@ def __init__( dirname = os.path.basename(self._directory) station_file = dirname + station_file # e.g. AirbaseStationList.csv station_filepath = os.path.join(self._directory, station_file) - if os.exists(station_filepath): + if os.path.exists(station_filepath): self._stations = self._read_station_list(station_filepath) else: raise Ascii2NetcdfTimeseriesReaderException( diff --git a/src/pyaro_readers/harpreader/harpreader.py b/src/pyaro_readers/harpreader/harpreader.py index 8fe4897..cde6696 100644 --- a/src/pyaro_readers/harpreader/harpreader.py +++ b/src/pyaro_readers/harpreader/harpreader.py @@ -73,6 +73,11 @@ def __init__( else: self._files.append(file) + def read(self): + """reading method""" + # check if the data has been read already + if len(self._data) != 0: + return bar = tqdm(total=len(self._files), disable=None) for f_idx, _file in enumerate(self._files): @@ -84,7 +89,7 @@ def __init__( # skip coordinate names if _var in self.COORD_NAMES: continue - if vars_to_read is not None and _var not in vars_to_read: + if self._vars_to_read is not None and _var not in self._vars_to_read: logger.info(f"Skipping {_var}") continue if _var not in self._data: @@ -214,12 +219,15 @@ def _unfiltered_variables(self) -> list[str]: list[str] The list of variable names. """ - return self._data.keys() + self.read() + return list(self._data.keys()) def _unfiltered_data(self, varname) -> Data: + self.read() return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: + self.read() return self._stations def close(self): diff --git a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py index 09696f3..942f213 100644 --- a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py +++ b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py @@ -45,6 +45,8 @@ def __init__( ): self._set_filters(filters) self._mode = mode + self._metadata = self.metadata() + if os.path.isdir(filename): self._directory = filename else: @@ -371,3 +373,6 @@ def description(self) -> str: def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() diff --git a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py index 226cdc0..2a6a3c6 100644 --- a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py +++ b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py @@ -73,25 +73,35 @@ def __init__( self._set_filters(filters) self._header = [] self._revision = datetime.datetime.min - - if Path(filename).is_file(): - self._filename = filename - self._process_file(self._filename, fill_country_flag) - - elif Path(filename).is_dir(): - files_pathlib = Path(filename).glob(file_mask) + self._filename = filename + self._fill_country_flag = fill_country_flag + self._file_mask = file_mask + self._tqdm_desc = tqdm_desc + + def read(self): + """read method""" + # check if the data has been read already + if len(self._data) != 0: + return + if Path(self._filename).is_file(): + self._process_file(self._filename, self._fill_country_flag) + + elif Path(self._filename).is_dir(): + files_pathlib = Path(self._filename).glob(self._file_mask) files = [x for x in files_pathlib if x.is_file()] if len(files) == 0: raise ValueError( f"Could not find any nas files in given folder {self._filename}" ) - bar = tqdm(desc=tqdm_desc, total=len(files), disable=None) + bar = tqdm(desc=self._tqdm_desc, total=len(files), disable=None) for file in files: bar.update(1) - self._process_file(file, fill_country_flag) + self._process_file(file, self._fill_country_flag) else: - raise ValueError(f"Given filename {filename} is neither a folder or a file") + raise ValueError( + f"Given filename {self._filename} is neither a folder or a file" + ) def _process_file(self, file: Path, fill_country_flag: bool = FILL_COUNTRY_FLAG): with open(file, newline="") as f: @@ -194,12 +204,15 @@ def metadata(self): # return metadata def _unfiltered_data(self, varname) -> Data: + self.read() return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: + self.read() return self._stations def _unfiltered_variables(self) -> list[str]: + self.read() return list(self._data.keys()) def close(self): diff --git a/src/pyaro_readers/nilupmfebas/EbasPmfReader.py b/src/pyaro_readers/nilupmfebas/EbasPmfReader.py index c3ec42a..51dcca9 100644 --- a/src/pyaro_readers/nilupmfebas/EbasPmfReader.py +++ b/src/pyaro_readers/nilupmfebas/EbasPmfReader.py @@ -45,6 +45,10 @@ def __init__( self._variables = {} self._metadata = {} self._revision = datetime.datetime.min + self._filename = filename + self._filemask = filemask + self._vars_to_read = vars_to_read + self._tqdm_desc = tqdm_desc # variable include filter comes like this # {'variables': {'include': ['PM10_density']}} @@ -55,26 +59,32 @@ def __init__( self._vars_to_read = vars_to_read logger.info(f"applying variable include filter {vars_to_read}...") - realpath = Path(filename).resolve() + self._realpath = Path(filename).resolve() - if Path(realpath).is_dir(): + def read(self): + """read method""" + + # check if the data has been read already + if len(self._data) != 0: + return + if Path(self._realpath).is_dir(): # search directory for files - files = list(realpath.glob(filemask)) - bar = tqdm(desc=tqdm_desc, total=len(files), disable=None) + files = list(self._realpath.glob(self._filemask)) + bar = tqdm(desc=self._tqdm_desc, total=len(files), disable=None) for _ridx, file in enumerate(files): bar.update(1) logger.info(file) - self.read_file(file, vars_to_read=vars_to_read) + self.read_file(file, vars_to_read=self._vars_to_read) if _ridx > 30: assert True bar.close() - elif Path(realpath).is_file(): - self.read_file(realpath) + elif Path(self._realpath).is_file(): + self.read_file(self._realpath) else: # filename is something else - raise EBASPMFReaderException(f"No such file or directory: {filename}") + raise EBASPMFReaderException(f"No such file or directory: {self._filename}") def metadata(self): metadata = dict() @@ -214,12 +224,15 @@ def read_file(self, filename: Path | str, vars_to_read: list[str] = None): ) def _unfiltered_data(self, varname) -> Data: + self.read() return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: + self.read() return self._stations def _unfiltered_variables(self) -> list[str]: + self.read() return list(self._data.keys()) def close(self): diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index 5f8ef09..3b50d0b 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -46,6 +46,23 @@ def test_dl_data_unzipped(self): self.assertEqual(len(ts.stations()), 4) self.assertGreaterEqual(int(ts.metadata()["revision"]), 220622120000) + # def test_dl_data_unzipped(self): + # if not self.external_resource_available(TEST_URL): + # self.skipTest(f"external resource not available: {TEST_URL}") + # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + # with engine.open( + # TEST_URL, + # filters=[], + # fill_country_flag=False, + # tqdm_desc="test_dl_data_unzipped", + # ) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertEqual(count, 49965) + # self.assertEqual(len(ts.stations()), 4) + # self.assertGreaterEqual(int(ts.metadata()["revision"]), 220622120000) + # def test_dl_data_zipped(self): if not self.external_resource_available(TEST_ZIP_URL): self.skipTest(f"external resource not available: {TEST_ZIP_URL}") @@ -128,6 +145,7 @@ def test_variables_filter(self): with engine.open( self.file, filters=[vfilter], tqdm_desc="test_variables_filter" ) as ts: + ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py new file mode 100644 index 0000000..a62092a --- /dev/null +++ b/tests/test_ActrisEbasReader.py @@ -0,0 +1,93 @@ +import unittest +import urllib.request + +import pyaro +import pyaro.timeseries +from pyaro.timeseries.Wrappers import VariableNameChangingReader + +TEST_URL = "https://prod-actris-md.nilu.no/Version" +VOCABULARY_URL = "https://prod-actris-md.nilu.no/V" + + +class TestActrisEbasTimeSeriesReader(unittest.TestCase): + engine = "actrisebas" + + station_filter = { + "stations": { + "include": ["Birkenes II", "Jungfraujoch", "Ispra", "Melpitz", "Westerland"] + }, + } + # vars_to_read = ["ozone mass concentration"] + # vars_to_read = ["aerosol particle sulphate mass concentration"] + vars_to_read = ["aerosol particle elemental carbon mass concentration"] + # pyaerocom_vars_to_read = ["conco3"] + pyaerocom_vars_to_read = ["vmro3"] + + # pyaerocom_vars_to_read = ["concso4t"] + + def test_api_online(self, url=TEST_URL): + try: + req = urllib.request.Request(url, method="HEAD") + resp = urllib.request.urlopen(req) + resp.url + return True + except: + return False + + def test_init(self): + engine = pyaro.list_timeseries_engines()[self.engine] + self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") + # just see that it doesn't fail + engine.description() + assert engine.args() + + def test_flag_list_online(self): + engine = pyaro.list_timeseries_engines()[self.engine] + + self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") + # just see that it doesn't fail + engine.description() + assert engine.args() + + def test_api_reading_small_data_set(self): + engine = pyaro.list_timeseries_engines()[self.engine] + with engine.open( + filters=self.station_filter, vars_to_read=self.vars_to_read + ) as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertGreaterEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertIn("revision", ts.metadata()) + + def test_api_reading_pyaerocom_naming(self): + # test access to the EBAS API + # test variable by variable + for _var in self.pyaerocom_vars_to_read: + engine = pyaro.list_timeseries_engines()[self.engine] + with engine.open(filters=self.station_filter, vars_to_read=[_var]) as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertGreaterEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) + self.assertIn("revision", ts.metadata()) + + def test_wrappers(self): + engine = pyaro.list_timeseries_engines()[self.engine] + new_var_name = "vmro3" + ebas_var_name = "ozone mass concentration" + with VariableNameChangingReader( + engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]), + reader_to_new={ebas_var_name: new_var_name}, + ) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertGreaterEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) + self.assertIn("revision", ts.metadata()) + pass + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_HARPReader.py b/tests/test_HARPReader.py index 2820d62..856de84 100644 --- a/tests/test_HARPReader.py +++ b/tests/test_HARPReader.py @@ -15,7 +15,7 @@ class TestHARPReader(unittest.TestCase): ) testdata_dir = ( - "/lustre/storeB/project/aerocom/aerocom1/AEROCOM_OBSDATA/CNEMC/aggregated/" + "/lustre/storeB/project/aerocom/aerocom1/AEROCOM_OBSDATA/SINCA/aggregated/" ) test_vars = ["PM10_density", "CO_volume_mixing_ratio", "PM2p5_density"] test_units = ["ug m-3", "ppm", "ug m-3"] diff --git a/tests/test_PyerocomBinding.py b/tests/test_PyerocomBinding.py new file mode 100644 index 0000000..0e84254 --- /dev/null +++ b/tests/test_PyerocomBinding.py @@ -0,0 +1,119 @@ +import unittest + + +class TestPyaroReaderPyaerocom(unittest.TestCase): + engine = "actrisebas" + + station_filter = { + "stations": { + "include": ["Birkenes II", "Jungfraujoch", "Ispra", "Melpitz", "Westerland"] + }, + } + AERONETVAR = "od440aer" + ACTRISEBASVAR = "concso4t" + ACTRISEBASVARLIST = ["concso4t", "concso4c"] + + def test_pyaerocom_aeronet(self): + # test reading via pyaerocom + try: + from pyaerocom.io.pyaro.pyaro_config import PyaroConfig + from pyaerocom.io import ReadUngridded + except ImportError: + assert "pyaerocom not installed" + return + + data_name = "aeronettest" + data_id = "aeronetsunreader" + url = "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv" + obsconfig = PyaroConfig( + name=data_name, + data_id=data_id, + filename_or_obj_or_url=url, + filters={"variables": {"include": ["AOD_440nm"]}}, + name_map={"AOD_440nm": self.AERONETVAR}, + ) + reader = ReadUngridded(f"{data_name}") + data = reader.read(vars_to_retrieve=self.AERONETVAR, configs=obsconfig) + self.assertGreaterEqual(len(data.unique_station_names), 4) + self.assertIn("Alta_Floresta", data.unique_station_names) + + def test_pyaerocom_actrisebas_single_var(self): + # test reading via pyaerocom + try: + from pyaerocom.io.pyaro.pyaro_config import PyaroConfig + from pyaerocom.io import ReadUngridded + except ImportError: + assert "pyaerocom not installed" + return + + data_name = "PYARO_actrisebas" + data_id = "actrisebas" + station_filter = { + "stations": { + "include": [ + "Birkenes II", + "Jungfraujoch", + "Ispra", + "Melpitz", + "Westerland", + ] + }, + } + # needs to be the variable name for actrisebas + url = self.ACTRISEBASVAR + obsconfig = PyaroConfig( + name=data_name, + data_id=data_id, + filename_or_obj_or_url=url, + filters=station_filter, + ) + reader = ReadUngridded(f"{data_name}") + data = reader.read(vars_to_retrieve=self.ACTRISEBASVAR, configs=obsconfig) + self.assertGreaterEqual(len(data.unique_station_names), 4) + self.assertIn("Ispra", data.unique_station_names) + self.assertIn(url, data.contains_vars) + + def test_pyaerocom_actrisebas_many_var(self): + # test multi var reading via pyaerocom + # not working properly atm as it's reading only one variable atm + try: + from pyaerocom.io.pyaro.pyaro_config import PyaroConfig + from pyaerocom.io import ReadUngridded + except ImportError: + assert "pyaerocom not installed" + return + + data_name = "PYARO_actrisebas" + data_id = "actrisebas" + station_filter = { + "stations": { + "include": [ + "Birkenes II", + "Jungfraujoch", + "Ispra", + "Melpitz", + "Westerland", + ] + }, + "variables": {"include": ["concso4t", "concso4c"]}, + } + # needs to be the variable name for actrisebas, but PyaroConfig wants this to a string and not a list + # (the pydantic setup is too pedantic) + url = self.ACTRISEBASVARLIST + obsconfig = PyaroConfig( + name=data_name, + data_id=data_id, + filename_or_obj_or_url=url, + filters=station_filter, + ) + reader = ReadUngridded(f"{data_name}") + data = reader.read(vars_to_retrieve=self.ACTRISEBASVAR, configs=obsconfig) + self.assertGreaterEqual(len(data.unique_station_names), 4) + self.assertIn("Ispra", data.unique_station_names) + self.assertIn(url[0], data.contains_vars) + # This does unfortunately not return the two variables asked for, but only the first: + self.assertIn(url[1], data.contains_vars) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/testdata/ACTRIS_EBAS/RTXS-U8P8.nc b/tests/testdata/ACTRIS_EBAS/RTXS-U8P8.nc new file mode 100644 index 0000000..b37fe88 --- /dev/null +++ b/tests/testdata/ACTRIS_EBAS/RTXS-U8P8.nc @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:673c713ec87233596679d0a5a5dd73874d191a3ffd878c31cbb9101c781a7ad3 +size 670835 diff --git a/tests/testdata/ACTRIS_EBAS/ozone mass concentration.json b/tests/testdata/ACTRIS_EBAS/ozone mass concentration.json new file mode 100644 index 0000000..d24175f --- /dev/null +++ b/tests/testdata/ACTRIS_EBAS/ozone mass concentration.json @@ -0,0 +1 @@ +[{"md_metadata":{"id":203110,"provider":{"name":"IN-SITU","atom":"http://localhost:5009/providers/14"},"file_identifier":"RTXS-U8P8.nc","language":"en","hierarchy_level":"dataset","online_resource":{"linkage":"http://ebas.nilu.no/"},"datestamp":"2024-06-13T22:00:00.0000000Z","created":"2024-06-14T08:00:07.0000000Z","contact":[{"first_name":"Markus","last_name":"Fiebig","organisation_name":"NILU","role_code":["custodian"],"country_code":"NO","delivery_point":"Instituttveien 18","address_city":"Kjeller","administrative_area":"Viken","postal_code":2007,"email":"ebas@nilu.no","position_name":"Senior Scientist"}]},"md_identification":{"abstract":"Ozone at Arkona. 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