From f64a23e34e0c73c5b367a53242a8500849523533 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 10:43:54 +0200 Subject: [PATCH 01/60] initial setup of ActrisEbas reader --- setup.cfg | 3 +- .../actrisebas/ActrisEbasReader.py | 277 ++++++++++++++++++ src/pyaro_readers/actrisebas/__init__.py | 4 + tests/test_ActrisEbasReader.py | 135 +++++++++ 4 files changed, 418 insertions(+), 1 deletion(-) create mode 100644 src/pyaro_readers/actrisebas/ActrisEbasReader.py create mode 100644 src/pyaro_readers/actrisebas/__init__.py create mode 100644 tests/test_ActrisEbasReader.py diff --git a/setup.cfg b/setup.cfg index 4217c98..2c9ca79 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.9.dev0 +version = 0.0.10.dev0 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md @@ -52,6 +52,7 @@ pyaro.timeseries = harp = pyaro_readers.harpreader:AeronetHARPEngine nilupmfabsorption = pyaro_readers.nilupmfabsorptionreader:NILUPMFAbsorptionTimeseriesEngine nilupmfebas = pyaro_readers.nilupmfebas:EbasPmfTimeseriesEngine + actrisebas = pyaro_readers.actrisebas:ActrisEbasTimeseriesEngine diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py new file mode 100644 index 0000000..5dc5767 --- /dev/null +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -0,0 +1,277 @@ +import csv +from io import BytesIO +from urllib.parse import urlparse +from urllib.request import urlopen +from zipfile import BadZipFile, ZipFile + +from geocoder_reverse_natural_earth import ( + Geocoder_Reverse_NE, + Geocoder_Reverse_Exception, +) +import numpy as np +import requests +from pyaro.timeseries import ( + AutoFilterReaderEngine, + Data, + Flag, + 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" +# number of lines to read before the reading is handed to Pythobn's csv reader +HEADER_LINE_NO = 7 +DELIMITER = "," +# +NAN_VAL = -999.0 +# update progress bar every N lines... +PG_UPDATE_LINES = 100 +# main variables to store +LAT_NAME = "Site_Latitude(Degrees)" +LON_NAME = "Site_Longitude(Degrees)" +ALT_NAME = "Site_Elevation(m)" +SITE_NAME = "AERONET_Site_Name" +DATE_NAME = "Date(dd:mm:yyyy)" +TIME_NAME: str = "Time(hh:mm:ss)" +AOD500_NAME = "AOD_500nm" +ANG4487_NAME = "440-870_Angstrom_Exponent" +AOD440_NAME = "AOD_440nm" +AOD870_NAME = "AOD_870nm" +AOD550_NAME = "AOD_550nm" + +DATA_VARS = [AOD500_NAME, ANG4487_NAME, AOD440_NAME, AOD870_NAME] +COMPUTED_VARS = [AOD550_NAME] +# 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 + +TS_TYPE_DIFFS = { + "daily": np.timedelta64(12, "h"), + "instantaneous": np.timedelta64(0, "s"), + "points": np.timedelta64(0, "s"), + "monthly": np.timedelta64(15, "D"), +} + + +class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): + def __init__( + self, + filename, + filters=[], + fill_country_flag: bool = FILL_COUNTRY_FLAG, + tqdm_desc: str | None = None, + ts_type: str = "daily", + ): + """open a new Aeronet timeseries-reader + + :param filename: str + :param filters: + :param fill_country_flag: + :param tqdm_desc: + :param filename_or_obj_or_url: path-like object to csv-file + + input file looks like this (daily file; times noted are middle times): + AERONET Version 3; + Cuiaba + Version 3: AOD Level 2.0 + The following data are automatically cloud cleared and quality assured with pre-field and post-field calibration applied. + Contact: PI=Pawan Gupta and Elena Lind; PI Email=Pawan.Gupta@nasa.gov and Elena.Lind@nasa.gov + Daily Averages,UNITS can be found at,,, https://aeronet.gsfc.nasa.gov/new_web/units.html + AERONET_Site,Date(dd:mm:yyyy),Time(hh:mm:ss),Day_of_Year,AOD_1640nm,AOD_1020nm,AOD_870nm,AOD_865nm,AOD_779nm,AOD_675nm,AOD_667nm,AOD_620nm,AOD_560nm,AOD_555nm,AOD_551nm,AOD_532nm,AOD_531nm,AOD_510nm,AOD_500nm,AOD_490nm,AOD_443nm,AOD_440nm,AOD_412nm,AOD_400nm,AOD_380nm,AOD_340nm,Precipitable_Water(cm),AOD_681nm,AOD_709nm,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,440-870_Angstrom_Exponent,380-500_Angstrom_Exponent,440-675_Angstrom_Exponent,500-870_Angstrom_Exponent,340-440_Angstrom_Exponent,440-675_Angstrom_Exponent[Polar],N[AOD_1640nm],N[AOD_1020nm],N[AOD_870nm],N[AOD_865nm],N[AOD_779nm],N[AOD_675nm],N[AOD_667nm],N[AOD_620nm],N[AOD_560nm],N[AOD_555nm],N[AOD_551nm],N[AOD_532nm],N[AOD_531nm],N[AOD_510nm],N[AOD_500nm],N[AOD_490nm],N[AOD_443nm],N[AOD_440nm],N[AOD_412nm],N[AOD_400nm],N[AOD_380nm],N[AOD_340nm],N[Precipitable_Water(cm)],N[AOD_681nm],N[AOD_709nm],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[440-870_Angstrom_Exponent],N[380-500_Angstrom_Exponent],N[440-675_Angstrom_Exponent],N[500-870_Angstrom_Exponent],N[340-440_Angstrom_Exponent],N[440-675_Angstrom_Exponent[Polar]],Data_Quality_Level,AERONET_Instrument_Number,AERONET_Site_Name,Site_Latitude(Degrees),Site_Longitude(Degrees),Site_Elevation(m) + Cuiaba,16:06:1993,12:00:00,167,-999.,0.081800,0.088421,-999.,-999.,0.095266,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.117581,-999.,-999.,-999.,0.149887,2.487799,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.424234,-999.,0.497630,-999.,0.924333,-999.,0,3,3,0,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,3,6,0,0,0,0,0,0,0,3,0,3,0,3,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 + Cuiaba,17:06:1993,12:00:00,168,-999.,0.092246,0.099877,-999.,-999.,0.110915,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.144628,-999.,-999.,-999.,0.187276,2.592902,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.547807,-999.,0.628609,-999.,0.988320,-999.,0,16,16,0,0,16,0,0,0,0,0,0,0,0,0,0,0,16,0,0,0,16,32,0,0,0,0,0,0,0,16,0,16,0,16,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 + """ + self._filename = filename + self._stations = {} + self._data = {} # var -> {data-array} + self._set_filters(filters) + self._header = [] + _laststatstr = "" + self._revision = datetime.datetime.min + # check if file is a URL + if self.is_valid_url(self._filename): + # try to open as zipfile + try: + r = requests.get(self._filename) + zip_ref = ZipFile(BytesIO(r.content)) + for file in zip_ref.namelist(): + with zip_ref.open(file) as response: + lines = [line.decode("utf-8") for line in response.readlines()] + # read only 1st file here + break + except BadZipFile: + response = urlopen(self._filename) + lines = [line.decode("utf-8") for line in response.readlines()] + + else: + with open(self._filename, newline="") as csvfile: + lines = csvfile.readlines() + + for _hidx in range(HEADER_LINE_NO - 1): + self._header.append(lines.pop(0)) + # get fields from header line although csv can do that as well since we might want to adjust these names + self._fields = lines.pop(0).strip().split(",") + + gcd = Geocoder_Reverse_NE() + crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) + bar = tqdm(desc=tqdm_desc, total=len(lines)) + for _ridx, row in enumerate(crd): + bar.update(1) + if row[SITE_NAME] != _laststatstr: + _laststatstr = row[SITE_NAME] + # new station + station = row[SITE_NAME] + lon = float(row[LON_NAME]) + lat = float(row[LAT_NAME]) + alt = float(row["Site_Elevation(m)"]) + if fill_country_flag: + try: + country = gcd.lookup(lat, lon)["ISO_A2_EH"] + except Geocoder_Reverse_Exception: + country = "NN" + else: + country = "NN" + + # units of Aeronet data are always 1 + units = "1" + if not station in self._stations: + self._stations[station] = Station( + { + "station": station, + "longitude": lon, + "latitude": lat, + "altitude": alt, + "country": country, + "url": "", + "long_name": station, + } + ) + # every line contains all variables, sometimes filled with NaNs though + if _ridx == 0: + for variable in DATA_VARS: + if variable in self._data: + da = self._data[variable] + if da.units != units: + raise Exception( + f"unit change from '{da.units}' to 'units'" + ) + else: + da = NpStructuredData(variable, units) + self._data[variable] = da + + day, month, year = row[DATE_NAME].split(":") + datestring = "-".join([year, month, day]) + datestring = "T".join([datestring, row[TIME_NAME]]) + self._revision = max( + [ + self._revision, + datetime.datetime.strptime(datestring, "%Y-%m-%dT%H:%M:%S"), + ] + ) + time_dummy = np.datetime64(datestring) + start = time_dummy - TS_TYPE_DIFFS[ts_type] + end = time_dummy + TS_TYPE_DIFFS[ts_type] + + ts_dummy_data = {} + for variable in DATA_VARS: + try: + value = float(row[variable]) + if value == NAN_VAL: + value = np.nan + # store value in ts_dummy_data, so we don't need to perform the nan check + # for each component of calculated values again + ts_dummy_data[variable] = value + except KeyError: + # computed variable + if variable == AOD550_NAME: + value = self.compute_od_from_angstromexp( + 0.55, + ts_dummy_data[AOD440_NAME], + 0.44, + ts_dummy_data[ANG4487_NAME], + ) + self._data[variable].append( + value, station, lat, lon, alt, start, end, Flag.VALID, np.nan + ) + bar.close() + + def metadata(self): + return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) + + def _unfiltered_data(self, varname) -> Data: + return self._data[varname] + + def _unfiltered_stations(self) -> dict[str, Station]: + return self._stations + + def _unfiltered_variables(self) -> list[str]: + return list(self._data.keys()) + + def close(self): + pass + + def compute_od_from_angstromexp( + self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float + ) -> float: + """Compute AOD at specified wavelength + + Uses Angstrom coefficient and reference AOD to compute the + corresponding wavelength shifted AOD + + Parameters + ---------- + to_lambda : :obj:`float` or :obj:`ndarray` + wavelength for which AOD is calculated + od_ref : :obj:`float` or :obj:`ndarray` + reference AOD + lambda_ref : :obj:`float` or :obj:`ndarray` + wavelength corresponding to reference AOD + angstrom_coeff : :obj:`float` or :obj:`ndarray` + Angstrom coefficient + + Returns + ------- + :obj:`float` or :obj:`ndarray` + AOD(s) at shifted wavelength + + """ + return od_ref * (lambda_ref / to_lambda) ** angstrom_coeff + + def calc_angstroem_coeff( + self, od1: float, od2: float, wl1: float, wl2: float + ) -> float: + """ + small helper method to calculate angstroem coefficient + + :param od1: + :param od2: + :param wl1: + :param wl2: + :return: + """ + return -np.log(od1 / od2) / np.log(wl1 / wl2) + + 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, filename, *args, **kwargs) -> ActrisEbasTimeSeriesReader: + return self.reader_class()(filename, *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..ff02509 --- /dev/null +++ b/src/pyaro_readers/actrisebas/__init__.py @@ -0,0 +1,4 @@ +from .ActrisEbasReader import ( + ActrisEbasReader, + ActrisEbasTimeseriesEngine, +) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py new file mode 100644 index 0000000..3914613 --- /dev/null +++ b/tests/test_ActrisEbasReader.py @@ -0,0 +1,135 @@ +import unittest +import urllib.request +import os + +import pyaro +import pyaro.timeseries +from pyaro.timeseries.Wrappers import VariableNameChangingReader + +TEST_URL = "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv" +TEST_ZIP_URL = ( + "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv.zip" +) +AERONETSUN_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" + + +class TestActrisEbasTimeSeriesReader(unittest.TestCase): + file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "testdata", + "aeronetsun_testdata.csv", + ) + + def external_resource_available(self, url): + try: + req = urllib.request.Request(TEST_URL, method="HEAD") + resp = urllib.request.urlopen(req) + resp.url + return True + except: + return False + + 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()["actrisebasreader"] + 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}") + engine = pyaro.list_timeseries_engines()["actrisebasreader"] + with engine.open( + TEST_ZIP_URL, + filters=[], + fill_country_flag=False, + tqdm_desc="test_dl_data_zipped", + ) 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_aeronet_data_zipped(self): + if not os.path.exists("/lustre"): + self.skipTest(f"lustre not available; skipping Aeronet download on CI") + + if not self.external_resource_available(AERONETSUN_URL): + self.skipTest(f"external resource not available: {AERONETSUN_URL}") + engine = pyaro.list_timeseries_engines()["actrisebasreader"] + with engine.open( + AERONETSUN_URL, + filters=[], + fill_country_flag=False, + tqdm_desc="aeronet data zipped", + ) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertGreaterEqual(count, 49965) + self.assertGreaterEqual(len(ts.stations()), 4) + self.assertGreaterEqual(int(ts.metadata()["revision"]), 240523120000) + + def test_init(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") + # just see that it doesn't fail + engine.description() + engine.args() + with engine.open( + self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" + ) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 49965) + self.assertEqual(len(ts.stations()), 4) + + def test_stationfilter(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) + with engine.open( + self.file, filters=[sfilter], tqdm_desc="test_stationfilter" + ) as ts: + count = 0 + for var in ts.variables(): + count += len(ts.data(var)) + self.assertEqual(count, 48775) + self.assertEqual(len(ts.stations()), 3) + + def test_wrappers(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + new_var_name = "od500aer" + with VariableNameChangingReader( + engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} + ) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + pass + + def test_variables_filter(self): + engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + new_var_name = "od550aer" + vfilter = pyaro.timeseries.filters.get( + "variables", reader_to_new={"AOD_550nm": new_var_name} + ) + with engine.open( + self.file, filters=[vfilter], tqdm_desc="test_variables_filter" + ) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + + +if __name__ == "__main__": + unittest.main() From 54767424334153fa42c57efbeaf3a928bd176ad4 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 10:55:06 +0200 Subject: [PATCH 02/60] make naming consistent --- setup.cfg | 2 +- src/pyaro_readers/actrisebas/__init__.py | 4 +- tests/test_ActrisEbasReader.py | 188 +++++++++++------------ 3 files changed, 97 insertions(+), 97 deletions(-) diff --git a/setup.cfg b/setup.cfg index 2c9ca79..77cfe26 100644 --- a/setup.cfg +++ b/setup.cfg @@ -52,7 +52,7 @@ pyaro.timeseries = harp = pyaro_readers.harpreader:AeronetHARPEngine nilupmfabsorption = pyaro_readers.nilupmfabsorptionreader:NILUPMFAbsorptionTimeseriesEngine nilupmfebas = pyaro_readers.nilupmfebas:EbasPmfTimeseriesEngine - actrisebas = pyaro_readers.actrisebas:ActrisEbasTimeseriesEngine + actrisebas = pyaro_readers.actrisebas:ActrisEbasTimeSeriesEngine diff --git a/src/pyaro_readers/actrisebas/__init__.py b/src/pyaro_readers/actrisebas/__init__.py index ff02509..d657bc1 100644 --- a/src/pyaro_readers/actrisebas/__init__.py +++ b/src/pyaro_readers/actrisebas/__init__.py @@ -1,4 +1,4 @@ from .ActrisEbasReader import ( - ActrisEbasReader, - ActrisEbasTimeseriesEngine, + ActrisEbasTimeSeriesReader, + ActrisEbasTimeSeriesEngine, ) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 3914613..c81eaf1 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -20,71 +20,71 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): "aeronetsun_testdata.csv", ) - def external_resource_available(self, url): - try: - req = urllib.request.Request(TEST_URL, method="HEAD") - resp = urllib.request.urlopen(req) - resp.url - return True - except: - return False - - 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()["actrisebasreader"] - 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}") - engine = pyaro.list_timeseries_engines()["actrisebasreader"] - with engine.open( - TEST_ZIP_URL, - filters=[], - fill_country_flag=False, - tqdm_desc="test_dl_data_zipped", - ) 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_aeronet_data_zipped(self): - if not os.path.exists("/lustre"): - self.skipTest(f"lustre not available; skipping Aeronet download on CI") - - if not self.external_resource_available(AERONETSUN_URL): - self.skipTest(f"external resource not available: {AERONETSUN_URL}") - engine = pyaro.list_timeseries_engines()["actrisebasreader"] - with engine.open( - AERONETSUN_URL, - filters=[], - fill_country_flag=False, - tqdm_desc="aeronet data zipped", - ) as ts: - count = 0 - for var in ts.variables(): - count += len(ts.data(var)) - self.assertGreaterEqual(count, 49965) - self.assertGreaterEqual(len(ts.stations()), 4) - self.assertGreaterEqual(int(ts.metadata()["revision"]), 240523120000) + # def external_resource_available(self, url): + # try: + # req = urllib.request.Request(TEST_URL, method="HEAD") + # resp = urllib.request.urlopen(req) + # resp.url + # return True + # except: + # return False + # + # 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()["actrisebasreader"] + # 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}") + # engine = pyaro.list_timeseries_engines()["actrisebasreader"] + # with engine.open( + # TEST_ZIP_URL, + # filters=[], + # fill_country_flag=False, + # tqdm_desc="test_dl_data_zipped", + # ) 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_aeronet_data_zipped(self): + # if not os.path.exists("/lustre"): + # self.skipTest(f"lustre not available; skipping Aeronet download on CI") + # + # if not self.external_resource_available(AERONETSUN_URL): + # self.skipTest(f"external resource not available: {AERONETSUN_URL}") + # engine = pyaro.list_timeseries_engines()["actrisebasreader"] + # with engine.open( + # AERONETSUN_URL, + # filters=[], + # fill_country_flag=False, + # tqdm_desc="aeronet data zipped", + # ) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertGreaterEqual(count, 49965) + # self.assertGreaterEqual(len(ts.stations()), 4) + # self.assertGreaterEqual(int(ts.metadata()["revision"]), 240523120000) def test_init(self): - engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + engine = pyaro.list_timeseries_engines()["actrisebasreader"] self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") # just see that it doesn't fail engine.description() @@ -98,37 +98,37 @@ def test_init(self): self.assertEqual(count, 49965) self.assertEqual(len(ts.stations()), 4) - def test_stationfilter(self): - engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) - with engine.open( - self.file, filters=[sfilter], tqdm_desc="test_stationfilter" - ) as ts: - count = 0 - for var in ts.variables(): - count += len(ts.data(var)) - self.assertEqual(count, 48775) - self.assertEqual(len(ts.stations()), 3) - - def test_wrappers(self): - engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - new_var_name = "od500aer" - with VariableNameChangingReader( - engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} - ) as ts: - self.assertEqual(ts.data(new_var_name).variable, new_var_name) - pass - - def test_variables_filter(self): - engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - new_var_name = "od550aer" - vfilter = pyaro.timeseries.filters.get( - "variables", reader_to_new={"AOD_550nm": new_var_name} - ) - with engine.open( - self.file, filters=[vfilter], tqdm_desc="test_variables_filter" - ) as ts: - self.assertEqual(ts.data(new_var_name).variable, new_var_name) + # def test_stationfilter(self): + # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + # sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) + # with engine.open( + # self.file, filters=[sfilter], tqdm_desc="test_stationfilter" + # ) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertEqual(count, 48775) + # self.assertEqual(len(ts.stations()), 3) + # + # def test_wrappers(self): + # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + # new_var_name = "od500aer" + # with VariableNameChangingReader( + # engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} + # ) as ts: + # self.assertEqual(ts.data(new_var_name).variable, new_var_name) + # pass + # + # def test_variables_filter(self): + # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] + # new_var_name = "od550aer" + # vfilter = pyaro.timeseries.filters.get( + # "variables", reader_to_new={"AOD_550nm": new_var_name} + # ) + # with engine.open( + # self.file, filters=[vfilter], tqdm_desc="test_variables_filter" + # ) as ts: + # self.assertEqual(ts.data(new_var_name).variable, new_var_name) if __name__ == "__main__": From 0c40de8e35f1ddd93d006e59a13782fa3afdf2d0 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 11:13:00 +0200 Subject: [PATCH 03/60] typo --- src/pyaro_readers/actrisebas/__init__.py | 2 +- tests/test_ActrisEbasReader.py | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/pyaro_readers/actrisebas/__init__.py b/src/pyaro_readers/actrisebas/__init__.py index d657bc1..e29df4d 100644 --- a/src/pyaro_readers/actrisebas/__init__.py +++ b/src/pyaro_readers/actrisebas/__init__.py @@ -1,4 +1,4 @@ -from .ActrisEbasReader import ( +from .ActrisEbasReader import ( ActrisEbasTimeSeriesReader, ActrisEbasTimeSeriesEngine, ) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index c81eaf1..64065c2 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -84,19 +84,19 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): # self.assertGreaterEqual(int(ts.metadata()["revision"]), 240523120000) def test_init(self): - engine = pyaro.list_timeseries_engines()["actrisebasreader"] + engine = pyaro.list_timeseries_engines()["actrisebas"] self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") # just see that it doesn't fail engine.description() engine.args() - with engine.open( - self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" - ) as ts: - count = 0 - for var in ts.variables(): - count += len(ts.data(var)) - self.assertEqual(count, 49965) - self.assertEqual(len(ts.stations()), 4) + # with engine.open( + # self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" + # ) as ts: + # count = 0 + # for var in ts.variables(): + # count += len(ts.data(var)) + # self.assertEqual(count, 49965) + # self.assertEqual(len(ts.stations()), 4) # def test_stationfilter(self): # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] From 089aa2d354c7afe839f6c803ac23bda75d2f4832 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 15:26:55 +0200 Subject: [PATCH 04/60] add response data for easy testing --- .../ozone_mass_concentration_formatted.json | 83700 ++++++++++++++++ 1 file changed, 83700 insertions(+) create mode 100644 tests/testdata/ACTRIS_EBAS/ozone_mass_concentration_formatted.json diff --git a/tests/testdata/ACTRIS_EBAS/ozone_mass_concentration_formatted.json b/tests/testdata/ACTRIS_EBAS/ozone_mass_concentration_formatted.json new file mode 100644 index 0000000..f268d72 --- /dev/null +++ b/tests/testdata/ACTRIS_EBAS/ozone_mass_concentration_formatted.json @@ -0,0 +1,83700 @@ +[ + { + "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. These measurements are gathered as a part of the following projects EMEP", + "title": "Ozone at Arkona", + "date_type": "creation", + "contact": [ + { + "first_name": "Yong", + "last_name": "Lin", + "organisation_name": "NILU", + "role_code": [ + "processor" + ], + "country_code": "NO", + "email": "ebas@nilu.no" + } + ], + "online_resource": { + "linkage": "https://ebas-data.nilu.no/" + }, + "identifier": { + "pid": "https://doi.org/10.48597/RTXS-U8P8", + "type": "DOI" + }, + "date": "2024-06-13T22:00:00.0000000Z" + }, + "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": ", EMEP, 1988-1989, Ozone at Arkona, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/RTXS-U8P8", + "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: EMEP." + }, + "md_keywords": { + "keywords": [ + "atmosphere", + "emep", + "gas phase", + "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": "suks", + "name": "Arkona", + "lat": 54.683333, + "lon": 13.433333, + "alt": 42, + "country_code": "DE", + "wmo_region": "Europe", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/suks" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 13.433333, + "east_bound_longitude": 13.433333, + "south_bound_latitude": 54.683333, + "north_bound_latitude": 54.683333 + }, + "ex_temporal_extent": { + "time_period_begin": "1987-12-31T23:00:00.0000000Z", + "time_period_end": "1989-12-30T23:00:00.0000000Z" + }, + "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/RT/XS/U8/RTXS-U8P8.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 670835 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/RT/XS/U8/RTXS-U8P8.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 670835 + } + ], + "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": [ + "EMEP" + ], + "variable_statistical_property": null, + "legacy_data": true, + "observation_timeliness": "scheduled", + "data_product": "full quality control", + "instrument_model": "Uv abs" + }, + "dq_data_quality_information": { + "compliance": "other" + }, + "provenance": { + "software": "https://git.nilu.no/ebas/ebas-io", + "version_history": null + } + }, + { + "md_metadata": { + "id": 203019, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "SGUS-M6X2.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-13T22:00:00.0000000Z", + "created": "2024-06-14T07:58:34.0000000Z", + "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 Ähtäri. 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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, + "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 + }, + { + "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 + } + ], + "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 + } + } +] From e024d1378d31e8574ed6492f8c773e9ec9be7bfe Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 16:27:09 +0200 Subject: [PATCH 05/60] add definition file for connection between pyaerocom <=> EBAS variables --- src/pyaro_readers/actrisebas/definitions.yaml | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 src/pyaro_readers/actrisebas/definitions.yaml diff --git a/src/pyaro_readers/actrisebas/definitions.yaml b/src/pyaro_readers/actrisebas/definitions.yaml new file mode 100644 index 0000000..3c091ae --- /dev/null +++ b/src/pyaro_readers/actrisebas/definitions.yaml @@ -0,0 +1,38 @@ +# connection between pyaerocom and ACTRIS-EBAS variables +variables: + #prototype + # - : + # actris_variable: + # - "ozone mass concentration" + # - "ozone amount fraction" + # actris_matrix: + # - "gas phase" + # ebas_component: + # - ozone + # ebas_matrix: + # - air + - vmro3: + actris_variable: + - "ozone mass concentration" + - "ozone amount fraction" + actris_matrix: + - "gas phase" + ebas_component: + - ozone + ebas_matrix: + - air + + - concso4: + actris_variable: + - "aerosol particle sulphate mass concentration" + actris_matrix: + - "aerosol particle phase" + - "PM10" + - "PM2.5" + ebas_component: + - "sulphate_corrected" + - "sulphate_total" + ebas_matrix: + - "aerosol" + - "pm10" + - "pm25" From 3f285695b27684215b7e9a733ad588d272c624b6 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 29 Aug 2024 16:36:14 +0200 Subject: [PATCH 06/60] add small netcdf file to testdata for local testing --- tests/testdata/ACTRIS_EBAS/RTXS-U8P8.nc | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 tests/testdata/ACTRIS_EBAS/RTXS-U8P8.nc 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 From 37a79702c7b85aa5f50f5adfec707d470475436d Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 3 Sep 2024 14:57:16 +0200 Subject: [PATCH 07/60] WIP: start simple --- .../actrisebas/ActrisEbasReader.py | 232 +++--------------- src/pyaro_readers/actrisebas/definitions.toml | 21 ++ src/pyaro_readers/actrisebas/definitions.yaml | 38 --- 3 files changed, 49 insertions(+), 242 deletions(-) create mode 100644 src/pyaro_readers/actrisebas/definitions.toml delete mode 100644 src/pyaro_readers/actrisebas/definitions.yaml diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 5dc5767..4d7cca1 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -1,15 +1,12 @@ -import csv +import logging +import tomllib from io import BytesIO from urllib.parse import urlparse from urllib.request import urlopen -from zipfile import BadZipFile, ZipFile -from geocoder_reverse_natural_earth import ( - Geocoder_Reverse_NE, - Geocoder_Reverse_Exception, -) import numpy as np import requests +import json from pyaro.timeseries import ( AutoFilterReaderEngine, Data, @@ -19,71 +16,33 @@ ) from tqdm import tqdm import datetime +import xarray as xr +import os -# default URL -BASE_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" -# number of lines to read before the reading is handed to Pythobn's csv reader -HEADER_LINE_NO = 7 -DELIMITER = "," -# -NAN_VAL = -999.0 -# update progress bar every N lines... -PG_UPDATE_LINES = 100 -# main variables to store -LAT_NAME = "Site_Latitude(Degrees)" -LON_NAME = "Site_Longitude(Degrees)" -ALT_NAME = "Site_Elevation(m)" -SITE_NAME = "AERONET_Site_Name" -DATE_NAME = "Date(dd:mm:yyyy)" -TIME_NAME: str = "Time(hh:mm:ss)" -AOD500_NAME = "AOD_500nm" -ANG4487_NAME = "440-870_Angstrom_Exponent" -AOD440_NAME = "AOD_440nm" -AOD870_NAME = "AOD_870nm" -AOD550_NAME = "AOD_550nm" - -DATA_VARS = [AOD500_NAME, ANG4487_NAME, AOD440_NAME, AOD870_NAME] -COMPUTED_VARS = [AOD550_NAME] -# 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 +logger = logging.getLogger(__name__) -TS_TYPE_DIFFS = { - "daily": np.timedelta64(12, "h"), - "instantaneous": np.timedelta64(0, "s"), - "points": np.timedelta64(0, "s"), - "monthly": np.timedelta64(15, "D"), -} +# default API URL base +# BASE_API_URL = "https://prod-actris-md.nilu.no/Vocabulary/categories" +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}/content/" +# basename of definitions.toml which connects the pyaerocom variable names with the ACTRIS variable names +DEFINITION_FILE_BASENAME = "definitions.toml" +DEFINITION_FILE = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + DEFINITION_FILE_BASENAME) class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, filename, filters=[], - fill_country_flag: bool = FILL_COUNTRY_FLAG, + var_name="ozone mass concentration", tqdm_desc: str | None = None, ts_type: str = "daily", ): - """open a new Aeronet timeseries-reader - - :param filename: str - :param filters: - :param fill_country_flag: - :param tqdm_desc: - :param filename_or_obj_or_url: path-like object to csv-file - - input file looks like this (daily file; times noted are middle times): - AERONET Version 3; - Cuiaba - Version 3: AOD Level 2.0 - The following data are automatically cloud cleared and quality assured with pre-field and post-field calibration applied. - Contact: PI=Pawan Gupta and Elena Lind; PI Email=Pawan.Gupta@nasa.gov and Elena.Lind@nasa.gov - Daily Averages,UNITS can be found at,,, https://aeronet.gsfc.nasa.gov/new_web/units.html - AERONET_Site,Date(dd:mm:yyyy),Time(hh:mm:ss),Day_of_Year,AOD_1640nm,AOD_1020nm,AOD_870nm,AOD_865nm,AOD_779nm,AOD_675nm,AOD_667nm,AOD_620nm,AOD_560nm,AOD_555nm,AOD_551nm,AOD_532nm,AOD_531nm,AOD_510nm,AOD_500nm,AOD_490nm,AOD_443nm,AOD_440nm,AOD_412nm,AOD_400nm,AOD_380nm,AOD_340nm,Precipitable_Water(cm),AOD_681nm,AOD_709nm,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,AOD_Empty,440-870_Angstrom_Exponent,380-500_Angstrom_Exponent,440-675_Angstrom_Exponent,500-870_Angstrom_Exponent,340-440_Angstrom_Exponent,440-675_Angstrom_Exponent[Polar],N[AOD_1640nm],N[AOD_1020nm],N[AOD_870nm],N[AOD_865nm],N[AOD_779nm],N[AOD_675nm],N[AOD_667nm],N[AOD_620nm],N[AOD_560nm],N[AOD_555nm],N[AOD_551nm],N[AOD_532nm],N[AOD_531nm],N[AOD_510nm],N[AOD_500nm],N[AOD_490nm],N[AOD_443nm],N[AOD_440nm],N[AOD_412nm],N[AOD_400nm],N[AOD_380nm],N[AOD_340nm],N[Precipitable_Water(cm)],N[AOD_681nm],N[AOD_709nm],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[AOD_Empty],N[440-870_Angstrom_Exponent],N[380-500_Angstrom_Exponent],N[440-675_Angstrom_Exponent],N[500-870_Angstrom_Exponent],N[340-440_Angstrom_Exponent],N[440-675_Angstrom_Exponent[Polar]],Data_Quality_Level,AERONET_Instrument_Number,AERONET_Site_Name,Site_Latitude(Degrees),Site_Longitude(Degrees),Site_Elevation(m) - Cuiaba,16:06:1993,12:00:00,167,-999.,0.081800,0.088421,-999.,-999.,0.095266,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.117581,-999.,-999.,-999.,0.149887,2.487799,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.424234,-999.,0.497630,-999.,0.924333,-999.,0,3,3,0,0,3,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,3,6,0,0,0,0,0,0,0,3,0,3,0,3,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 - Cuiaba,17:06:1993,12:00:00,168,-999.,0.092246,0.099877,-999.,-999.,0.110915,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.144628,-999.,-999.,-999.,0.187276,2.592902,-999.,-999.,-999.,-999.,-999.,-999.,-999.,0.547807,-999.,0.628609,-999.,0.988320,-999.,0,16,16,0,0,16,0,0,0,0,0,0,0,0,0,0,0,16,0,0,0,16,32,0,0,0,0,0,0,0,16,0,16,0,16,0,lev20,3,Cuiaba,-15.555244,-56.070214,234.000000 + """ """ self._filename = filename self._stations = {} @@ -92,112 +51,11 @@ def __init__( self._header = [] _laststatstr = "" self._revision = datetime.datetime.min - # check if file is a URL - if self.is_valid_url(self._filename): - # try to open as zipfile - try: - r = requests.get(self._filename) - zip_ref = ZipFile(BytesIO(r.content)) - for file in zip_ref.namelist(): - with zip_ref.open(file) as response: - lines = [line.decode("utf-8") for line in response.readlines()] - # read only 1st file here - break - except BadZipFile: - response = urlopen(self._filename) - lines = [line.decode("utf-8") for line in response.readlines()] - - else: - with open(self._filename, newline="") as csvfile: - lines = csvfile.readlines() - - for _hidx in range(HEADER_LINE_NO - 1): - self._header.append(lines.pop(0)) - # get fields from header line although csv can do that as well since we might want to adjust these names - self._fields = lines.pop(0).strip().split(",") - - gcd = Geocoder_Reverse_NE() - crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) - bar = tqdm(desc=tqdm_desc, total=len(lines)) - for _ridx, row in enumerate(crd): - bar.update(1) - if row[SITE_NAME] != _laststatstr: - _laststatstr = row[SITE_NAME] - # new station - station = row[SITE_NAME] - lon = float(row[LON_NAME]) - lat = float(row[LAT_NAME]) - alt = float(row["Site_Elevation(m)"]) - if fill_country_flag: - try: - country = gcd.lookup(lat, lon)["ISO_A2_EH"] - except Geocoder_Reverse_Exception: - country = "NN" - else: - country = "NN" - - # units of Aeronet data are always 1 - units = "1" - if not station in self._stations: - self._stations[station] = Station( - { - "station": station, - "longitude": lon, - "latitude": lat, - "altitude": alt, - "country": country, - "url": "", - "long_name": station, - } - ) - # every line contains all variables, sometimes filled with NaNs though - if _ridx == 0: - for variable in DATA_VARS: - if variable in self._data: - da = self._data[variable] - if da.units != units: - raise Exception( - f"unit change from '{da.units}' to 'units'" - ) - else: - da = NpStructuredData(variable, units) - self._data[variable] = da + # read config file + self._def_data = self._read_definitions(file=DEFINITION_FILE) - day, month, year = row[DATE_NAME].split(":") - datestring = "-".join([year, month, day]) - datestring = "T".join([datestring, row[TIME_NAME]]) - self._revision = max( - [ - self._revision, - datetime.datetime.strptime(datestring, "%Y-%m-%dT%H:%M:%S"), - ] - ) - time_dummy = np.datetime64(datestring) - start = time_dummy - TS_TYPE_DIFFS[ts_type] - end = time_dummy + TS_TYPE_DIFFS[ts_type] - - ts_dummy_data = {} - for variable in DATA_VARS: - try: - value = float(row[variable]) - if value == NAN_VAL: - value = np.nan - # store value in ts_dummy_data, so we don't need to perform the nan check - # for each component of calculated values again - ts_dummy_data[variable] = value - except KeyError: - # computed variable - if variable == AOD550_NAME: - value = self.compute_od_from_angstromexp( - 0.55, - ts_dummy_data[AOD440_NAME], - 0.44, - ts_dummy_data[ANG4487_NAME], - ) - self._data[variable].append( - value, station, lat, lon, alt, start, end, Flag.VALID, np.nan - ) - bar.close() + # bar = tqdm(desc=tqdm_desc, total=len(lines)) + # bar.close() def metadata(self): return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) @@ -214,46 +72,12 @@ def _unfiltered_variables(self) -> list[str]: def close(self): pass - def compute_od_from_angstromexp( - self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float - ) -> float: - """Compute AOD at specified wavelength - - Uses Angstrom coefficient and reference AOD to compute the - corresponding wavelength shifted AOD - - Parameters - ---------- - to_lambda : :obj:`float` or :obj:`ndarray` - wavelength for which AOD is calculated - od_ref : :obj:`float` or :obj:`ndarray` - reference AOD - lambda_ref : :obj:`float` or :obj:`ndarray` - wavelength corresponding to reference AOD - angstrom_coeff : :obj:`float` or :obj:`ndarray` - Angstrom coefficient - - Returns - ------- - :obj:`float` or :obj:`ndarray` - AOD(s) at shifted wavelength - - """ - return od_ref * (lambda_ref / to_lambda) ** angstrom_coeff - - def calc_angstroem_coeff( - self, od1: float, od2: float, wl1: float, wl2: float - ) -> float: - """ - small helper method to calculate angstroem coefficient - - :param od1: - :param od2: - :param wl1: - :param wl2: - :return: - """ - return -np.log(od1 / od2) / np.log(wl1 / wl2) + 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: diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml new file mode 100644 index 0000000..b1194a0 --- /dev/null +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -0,0 +1,21 @@ +# 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.vmro3] +actris_variable = ["ozone mass concentration", "ozone amount fraction"] +actris_matrix = ["gas phase"] +ebas_component = ["ozone"] +ebas_matrix = ["air"] + +[variables.concso4] +actris_variable = ["aerosol particle sulphate mass concentration"] +actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] +ebas_component = ["sulphate_corrected", "sulphate_total"] +ebas_matrix = ["aerosol", "pm10", "pm25"] diff --git a/src/pyaro_readers/actrisebas/definitions.yaml b/src/pyaro_readers/actrisebas/definitions.yaml deleted file mode 100644 index 3c091ae..0000000 --- a/src/pyaro_readers/actrisebas/definitions.yaml +++ /dev/null @@ -1,38 +0,0 @@ -# connection between pyaerocom and ACTRIS-EBAS variables -variables: - #prototype - # - : - # actris_variable: - # - "ozone mass concentration" - # - "ozone amount fraction" - # actris_matrix: - # - "gas phase" - # ebas_component: - # - ozone - # ebas_matrix: - # - air - - vmro3: - actris_variable: - - "ozone mass concentration" - - "ozone amount fraction" - actris_matrix: - - "gas phase" - ebas_component: - - ozone - ebas_matrix: - - air - - - concso4: - actris_variable: - - "aerosol particle sulphate mass concentration" - actris_matrix: - - "aerosol particle phase" - - "PM10" - - "PM2.5" - ebas_component: - - "sulphate_corrected" - - "sulphate_total" - ebas_matrix: - - "aerosol" - - "pm10" - - "pm25" From 14190d7728c42d612c0fc940dddc9284c5ac06ab Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Wed, 4 Sep 2024 14:30:03 +0200 Subject: [PATCH 08/60] WIP: try reading actual data --- setup.cfg | 2 +- .../actrisebas/ActrisEbasReader.py | 60 ++++++++++--- tests/test_ActrisEbasReader.py | 88 ++++--------------- 3 files changed, 66 insertions(+), 84 deletions(-) diff --git a/setup.cfg b/setup.cfg index 77cfe26..6dfb116 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.10.dev0 +version = 0.0.10.dev1 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 4d7cca1..777a51d 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -1,8 +1,10 @@ import logging import tomllib from io import BytesIO -from urllib.parse import urlparse +from urllib.parse import urlparse, quote from urllib.request import urlopen +from urllib3.util.retry import Retry +from urllib3.poolmanager import PoolManager import numpy as np import requests @@ -25,26 +27,33 @@ # BASE_API_URL = "https://prod-actris-md.nilu.no/Vocabulary/categories" 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}/content/" +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" DEFINITION_FILE = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - DEFINITION_FILE_BASENAME) + os.path.dirname(os.path.realpath(__file__)), DEFINITION_FILE_BASENAME +) + +# number of times an api request is tried before we consider it failed +MAX_RETRIES = 2 + + +class ActrisEbasRetryException(Exception): + pass + class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, - filename, + # filename, filters=[], var_name="ozone mass concentration", tqdm_desc: str | None = None, ts_type: str = "daily", ): - """ - """ - self._filename = filename + """ """ + self._filename = None self._stations = {} self._data = {} # var -> {data-array} self._set_filters(filters) @@ -53,9 +62,30 @@ def __init__( self._revision = datetime.datetime.min # read config file self._def_data = self._read_definitions(file=DEFINITION_FILE) - - # bar = tqdm(desc=tqdm_desc, total=len(lines)) - # bar.close() + if not isinstance(var_name, list): + var_name = [var_name] + + for var in var_name: + # search for variable metadata + query_url = f"{VAR_QUERY_URL}{quote(var)}" + retries = Retry(connect=5, read=2, redirect=5) + http = PoolManager(retries=retries) + response = http.request("GET", query_url) + + # retry_counter = MAX_RETRIES + # while retry_counter > 0: + # try: + # response = requests.get(query_url) + # response.raise_for_status() # raises an HTTPError if the status code is >= 400 + # except requests.exceptions.HTTPError as err: + # print(f"Error: {err}") + + # text_resp = response.data.decode('utf-8') + json_resp = json.loads(response.data.decode("utf-8")) + print(json_resp) + + bar = tqdm(desc=tqdm_desc, total=len(lines)) + bar.close() def metadata(self): return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) @@ -75,7 +105,7 @@ def close(self): 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: + with open(file, "rb") as fh: tmp = tomllib.load(fh) return tmp @@ -91,8 +121,10 @@ class ActrisEbasTimeSeriesEngine(AutoFilterReaderEngine.AutoFilterEngine): def reader_class(self): return ActrisEbasTimeSeriesReader - def open(self, filename, *args, **kwargs) -> ActrisEbasTimeSeriesReader: - return self.reader_class()(filename, *args, **kwargs) + # def open(self, filename, *args, **kwargs) -> ActrisEbasTimeSeriesReader: + def open(self, *args, **kwargs) -> ActrisEbasTimeSeriesReader: + # return self.reader_class()(filename, *args, **kwargs) + return self.reader_class()(*args, **kwargs) def description(self): return "ACTRIS EBAS reader using the pyaro infrastructure" diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 64065c2..072c110 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -6,7 +6,8 @@ import pyaro.timeseries from pyaro.timeseries.Wrappers import VariableNameChangingReader -TEST_URL = "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv" +TEST_URL = "https://prod-actris-md.nilu.no/Version" +VOCABULARY_URL = "https://prod-actris-md.nilu.no/V" TEST_ZIP_URL = ( "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv.zip" ) @@ -14,13 +15,17 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): - file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "testdata", - "aeronetsun_testdata.csv", - ) - # def external_resource_available(self, url): + def test_api_online(self, url=TEST_URL): + try: + req = urllib.request.Request(TEST_URL, method="HEAD") + resp = urllib.request.urlopen(req) + resp.url + return True + except: + return False + + # def test_vocabulary(self, url=TEST_URL): # try: # req = urllib.request.Request(TEST_URL, method="HEAD") # resp = urllib.request.urlopen(req) @@ -29,75 +34,20 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): # except: # return False # - # 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()["actrisebasreader"] - # 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}") - # engine = pyaro.list_timeseries_engines()["actrisebasreader"] - # with engine.open( - # TEST_ZIP_URL, - # filters=[], - # fill_country_flag=False, - # tqdm_desc="test_dl_data_zipped", - # ) 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_aeronet_data_zipped(self): - # if not os.path.exists("/lustre"): - # self.skipTest(f"lustre not available; skipping Aeronet download on CI") - # - # if not self.external_resource_available(AERONETSUN_URL): - # self.skipTest(f"external resource not available: {AERONETSUN_URL}") - # engine = pyaro.list_timeseries_engines()["actrisebasreader"] - # with engine.open( - # AERONETSUN_URL, - # filters=[], - # fill_country_flag=False, - # tqdm_desc="aeronet data zipped", - # ) as ts: - # count = 0 - # for var in ts.variables(): - # count += len(ts.data(var)) - # self.assertGreaterEqual(count, 49965) - # self.assertGreaterEqual(len(ts.stations()), 4) - # self.assertGreaterEqual(int(ts.metadata()["revision"]), 240523120000) def test_init(self): engine = pyaro.list_timeseries_engines()["actrisebas"] self.assertEqual(engine.url(), "https://github.com/metno/pyaro-readers") # just see that it doesn't fail engine.description() - engine.args() - # with engine.open( - # self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" - # ) as ts: - # count = 0 - # for var in ts.variables(): - # count += len(ts.data(var)) - # self.assertEqual(count, 49965) - # self.assertEqual(len(ts.stations()), 4) + assert engine.args() + def test_api_reading(self): + # test access to the EBAS API + engine = pyaro.list_timeseries_engines()["actrisebas"] + with engine.open(var_name="ozone mass concentration", filters=[]) as ts: + # test that the definitions file could be read properly + self.assertGreaterEqual((len(ts._def_data)['variables'], 2)) # def test_stationfilter(self): # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] # sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) From 49a99a6e6aaff2ab0220b2fbee48e7dbb9253a87 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 6 Sep 2024 15:42:05 +0200 Subject: [PATCH 09/60] WIP after reading 1st data file --- setup.cfg | 2 +- .../actrisebas/ActrisEbasReader.py | 148 +++++++++++++++--- src/pyaro_readers/actrisebas/definitions.toml | 2 + tests/test_ActrisEbasReader.py | 9 ++ 4 files changed, 141 insertions(+), 20 deletions(-) diff --git a/setup.cfg b/setup.cfg index 6dfb116..9dd3126 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.10.dev1 +version = 0.0.10.dev2 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 777a51d..c533f7c 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -3,6 +3,8 @@ from io import BytesIO from urllib.parse import urlparse, quote from urllib.request import urlopen + +from matplotlib.font_manager import json_load from urllib3.util.retry import Retry from urllib3.poolmanager import PoolManager @@ -38,39 +40,78 @@ # 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 ActrisEbasTestDataNotFoundException(Exception): + pass + class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( - self, + self, # filename, - filters=[], - var_name="ozone mass concentration", - tqdm_desc: str | None = None, - ts_type: str = "daily", + filters=[], + vars_to_read: str = "ozone mass concentration", + tqdm_desc: str | None = None, + ts_type: str = "daily", + test_flag: bool = True, + sites_to_read: list[str] = None, # for testing ): """ """ self._filename = None self._stations = {} - self._data = {} # var -> {data-array} + self._urls_to_dl = {} + self._data = {} # var -> {data-array} self._set_filters(filters) self._header = [] _laststatstr = "" self._revision = datetime.datetime.min # read config file self._def_data = self._read_definitions(file=DEFINITION_FILE) - if not isinstance(var_name, list): - var_name = [var_name] - - for var in var_name: - # search for variable metadata - query_url = f"{VAR_QUERY_URL}{quote(var)}" - retries = Retry(connect=5, read=2, redirect=5) - http = PoolManager(retries=retries) - response = http.request("GET", query_url) + if not isinstance(vars_to_read, list): + vars_to_read = [vars_to_read] + + for var in vars_to_read: + # for testing since the API is error-prone and slow + if test_flag: + test_file = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "..", "..", "..", "tests", "testdata", "ACTRIS_EBAS", + f"{var}.json", + ) + if not os.path.exists(test_file): + raise ActrisEbasTestDataNotFoundException(f"test file not found: {test_file}") + json_resp = json_load(test_file) + else: + # search for variable metadata + query_url = f"{VAR_QUERY_URL}{quote(var)}" + retries = Retry(connect=5, read=2, redirect=5) + http = PoolManager(retries=retries) + response = http.request("GET", query_url) + + json_resp = json.loads(response.data.decode("utf-8")) + + self._urls_to_dl[var] = self.extract_urls(json_resp, sites_to_read=sites_to_read) + self._data[var] = self.read_data(self._urls_to_dl[var]) # retry_counter = MAX_RETRIES # while retry_counter > 0: @@ -81,15 +122,84 @@ def __init__( # print(f"Error: {err}") # text_resp = response.data.decode('utf-8') - json_resp = json.loads(response.data.decode("utf-8")) - print(json_resp) - bar = tqdm(desc=tqdm_desc, total=len(lines)) - bar.close() def metadata(self): return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) + + def read_data(self, urls_to_dl: dict, tqdm_desc="file reading", sites_to_read: list[str] = None): + ''' + read the data from EBAS threadds server + + ''' + bar = tqdm(desc=tqdm_desc, total=len(urls_to_dl)) + for s_idx, site_name in enumerate(urls_to_dl): + for f_idx, url in enumerate(urls_to_dl[site_name]): + tmp_data = xr.open_dataset(url) + # create times... + start_time = np.asarray(tmp_data["time_bnds"][:,0]) + end_time = np.asarray(tmp_data["time_bnds"][:,1]) + ts_no = len(start_time) + lat = np.full(ts_no, tmp_data.attrs["geospatial_lat_min"]) + long = np.full(ts_no, tmp_data.attrs["geospatial_lon_min"]) + station = np.full(ts_no, tmp_data.attrs["ebas_station_name"]) + altitude = np.full(ts_no, tmp_data.attrs["geospatial_vertical_min"]) + standard_deviation = np.full(ts_no, np.NAN) + + # put all data variables in the data struct for the moment + for _data_var in self._get_ebas_data_vars(tmp_data): + vals = tmp_data[_data_var].values + flags = np.full(ts_no, Flag.VALID) + if _data_var not in self._data: + self._data[_data_var] = [] + + + bar.update(1) + bar.close() + + + 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: + data_vars.append(data_var) + + return data_vars + + def extract_urls(self, json_resp: dict, sites_to_read: list[str]=None) -> 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] + # temporary + if sites_to_read is not None and site_name in sites_to_read: + 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: + continue + else: + urls_to_dl[site_name].append(distribution_data[DISTRIBUTION_URL_KEY]) + break + return urls_to_dl + def _unfiltered_data(self, varname) -> Data: return self._data[varname] diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index b1194a0..36fe1d0 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -13,9 +13,11 @@ actris_variable = ["ozone mass concentration", "ozone amount fraction"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] +ebas_unit = "ug/m3" [variables.concso4] actris_variable = ["aerosol particle sulphate mass concentration"] actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] ebas_component = ["sulphate_corrected", "sulphate_total"] ebas_matrix = ["aerosol", "pm10", "pm25"] +ebas_unit = "ug/m3" \ No newline at end of file diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 072c110..e1deb74 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -48,6 +48,15 @@ def test_api_reading(self): with engine.open(var_name="ozone mass concentration", filters=[]) as ts: # test that the definitions file could be read properly self.assertGreaterEqual((len(ts._def_data)['variables'], 2)) + + def test_api_reading_Birkenes(self): + # test access to the EBAS API + engine = pyaro.list_timeseries_engines()["actrisebas"] + # sfilter = pyaro.timeseries.filters.get("stations", include=["Birkenes II"]) + with engine.open(vars_to_read="ozone mass concentration", filters=[], sites_to_read=["Birkenes II"]) as ts: + # test that the definitions file could be read properly + self.assertGreaterEqual((len(ts._def_data)['variables'], 2)) + # def test_stationfilter(self): # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] # sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) From 964d3bce16649d5ffdab5e085a871da186d03a46 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Sun, 8 Sep 2024 22:16:28 +0200 Subject: [PATCH 10/60] added another cache file --- tests/testdata/ACTRIS_EBAS/ozone mass concentration.json | 1 + 1 file changed, 1 insertion(+) create mode 100644 tests/testdata/ACTRIS_EBAS/ozone mass concentration.json 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 @@ 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return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) + return self._metadata def read_data(self, urls_to_dl: dict, tqdm_desc="file reading", sites_to_read: list[str] = None): From bb45f75dd6eb588c196f1ec80eccea45b49beb34 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:12:25 +0200 Subject: [PATCH 12/60] WIP: 1st version with passing tests --- .../actrisebas/ActrisEbasReader.py | 164 ++++++++++++------ tests/test_ActrisEbasReader.py | 44 +++-- 2 files changed, 140 insertions(+), 68 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 81c86da..a077fc3 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -4,7 +4,6 @@ from urllib.parse import urlparse, quote from urllib.request import urlopen -from matplotlib.font_manager import json_load from urllib3.util.retry import Retry from urllib3.poolmanager import PoolManager @@ -58,9 +57,11 @@ # should be "time" as of CF convention, but other names can be added here TIME_VAR_NAME = ["time"] + class ActrisEbasRetryException(Exception): pass + class ActrisEbasTestDataNotFoundException(Exception): pass @@ -68,43 +69,64 @@ class ActrisEbasTestDataNotFoundException(Exception): class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, - # filename, filters=[], - vars_to_read: str = "ozone mass concentration", tqdm_desc: str | None = None, ts_type: str = "daily", test_flag: bool = True, - sites_to_read: list[str] = None, # for testing ): """ """ self._filename = None self._stations = {} self._urls_to_dl = {} - self._data = {} # var -> {data-array} + self._data = {} # var -> {data-array} self._set_filters(filters) self._header = [] self._metadata = {} _laststatstr = "" self._revision = datetime.datetime.min - self._metadata['revision'] = datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S") + self._metadata["revision"] = datetime.datetime.strftime( + self._revision, "%y%m%d%H%M%S" + ) + + try: + vars_to_read = filters["variables"]["include"] + except KeyError: + raise ValueError( + f"As of now, you have to give the species you want to read in filter.variables.include" + ) + + try: + sites_to_read = filters["stations"]["include"] + except KeyError: + sites_to_read = [] + + try: + sites_to_exclude = filters["stations"]["exclude"] + except KeyError: + sites_to_exclude = [] # read config file self._def_data = self._read_definitions(file=DEFINITION_FILE) - if not isinstance(vars_to_read, list): - vars_to_read = [vars_to_read] - for var in vars_to_read: self._metadata[var] = {} # for testing since the API is error-prone and slow if test_flag: test_file = os.path.join( os.path.dirname(os.path.realpath(__file__)), - "..", "..", "..", "tests", "testdata", "ACTRIS_EBAS", - f"{var}.json", + "..", + "..", + "..", + "tests", + "testdata", + "ACTRIS_EBAS", + f"{var}.json", ) if not os.path.exists(test_file): - raise ActrisEbasTestDataNotFoundException(f"test file not found: {test_file}") - json_resp = json_load(test_file) + raise ActrisEbasTestDataNotFoundException( + f"test file not found: {test_file}" + ) + with open(test_file, "r") as f: + json_resp = json.load(f) else: # search for variable metadata query_url = f"{VAR_QUERY_URL}{quote(var)}" @@ -115,39 +137,35 @@ def __init__( json_resp = json.loads(response.data.decode("utf-8")) self._metadata[var] = json_resp - self._urls_to_dl[var] = self.extract_urls(json_resp, sites_to_read=sites_to_read) + self._urls_to_dl[var] = self.extract_urls( + json_resp, + sites_to_read=sites_to_read, + sites_to_exclude=sites_to_exclude, + ) self._data[var] = self.read_data(self._urls_to_dl[var]) - # retry_counter = MAX_RETRIES - # while retry_counter > 0: - # try: - # response = requests.get(query_url) - # response.raise_for_status() # raises an HTTPError if the status code is >= 400 - # except requests.exceptions.HTTPError as err: - # print(f"Error: {err}") - - # text_resp = response.data.decode('utf-8') - - def metadata(self): return self._metadata - - def read_data(self, urls_to_dl: dict, tqdm_desc="file reading", sites_to_read: list[str] = None): - ''' - read the data from EBAS threadds server - - ''' + def read_data( + self, + urls_to_dl: dict, + tqdm_desc="reading stations", + sites_to_read: list[str] = None, + ): + """ + read the data from EBAS thredds server + """ bar = tqdm(desc=tqdm_desc, total=len(urls_to_dl)) for s_idx, site_name in enumerate(urls_to_dl): for f_idx, url in enumerate(urls_to_dl[site_name]): tmp_data = xr.open_dataset(url) # create times... - start_time = np.asarray(tmp_data["time_bnds"][:,0]) - end_time = np.asarray(tmp_data["time_bnds"][:,1]) + 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"]) - long = np.full(ts_no, tmp_data.attrs["geospatial_lon_min"]) + lon = np.full(ts_no, tmp_data.attrs["geospatial_lon_min"]) station = np.full(ts_no, tmp_data.attrs["ebas_station_name"]) altitude = np.full(ts_no, tmp_data.attrs["geospatial_vertical_min"]) standard_deviation = np.full(ts_no, np.NAN) @@ -157,21 +175,54 @@ def read_data(self, urls_to_dl: dict, tqdm_desc="file reading", sites_to_read: l vals = tmp_data[_data_var].values flags = np.full(ts_no, Flag.VALID) if _data_var not in self._data: - self._data[_data_var] = [] - - + self._data[_data_var] = NpStructuredData( + _data_var, self.get_ebas_data_units(tmp_data, _data_var) + ) + + self._data[_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, + ) + if not site_name in self._stations: + self._stations[site_name] = Station( + { + "station": site_name, + "longitude": lon[0], + "latitude": lat[0], + "altitude": altitude[0], + "country": self.get_ebas_data_country_code(tmp_data), + "url": "", + "long_name": site_name, + } + ) bar.update(1) bar.close() + 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_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_ebas_data_vars(self, tmp_data, actris_var:str = None, units:str = None): - ''' + 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: @@ -182,26 +233,41 @@ def _get_ebas_data_vars(self, tmp_data, actris_var:str = None, units:str = None) return data_vars - def extract_urls(self, json_resp: dict, sites_to_read: list[str]=None) -> dict: - ''' + 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] - # temporary - if sites_to_read is not None and site_name in sites_to_read: + site_name = site_data[LOCATION_ROOT_KEY][LOCATION_FACILITY_KEY][ + LOCATION_NAME_KEY + ] + if site_name in sites_to_exclude: + 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: + for url_idx, distribution_data in enumerate( + site_data[DISTRIBUTION_ROOT_KEY] + ): + if ( + distribution_data[DISTRIBUTION_PROTOCOL_KEY] + != DISTRIBUTION_PROTOCOL_NAME + ): continue else: - urls_to_dl[site_name].append(distribution_data[DISTRIBUTION_URL_KEY]) + urls_to_dl[site_name].append( + distribution_data[DISTRIBUTION_URL_KEY] + ) break return urls_to_dl diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index e1deb74..87ea564 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -8,13 +8,9 @@ TEST_URL = "https://prod-actris-md.nilu.no/Version" VOCABULARY_URL = "https://prod-actris-md.nilu.no/V" -TEST_ZIP_URL = ( - "https://pyaerocom.met.no/pyaro-suppl/testdata/aeronetsun_testdata.csv.zip" -) -AERONETSUN_URL = "https://aeronet.gsfc.nasa.gov/data_push/V3/All_Sites_Times_Daily_Averages_AOD20.zip" - class TestActrisEbasTimeSeriesReader(unittest.TestCase): + engine = "actrisebas" def test_api_online(self, url=TEST_URL): try: @@ -36,26 +32,36 @@ def test_api_online(self, url=TEST_URL): # def test_init(self): - engine = pyaro.list_timeseries_engines()["actrisebas"] + 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(self): - # test access to the EBAS API - engine = pyaro.list_timeseries_engines()["actrisebas"] - with engine.open(var_name="ozone mass concentration", filters=[]) as ts: - # test that the definitions file could be read properly - self.assertGreaterEqual((len(ts._def_data)['variables'], 2)) - - def test_api_reading_Birkenes(self): + # def test_api_reading(self): + # # test access to the EBAS API + # filters={"variables": {"include": ["ozone mass concentration", ]}} + # engine = pyaro.list_timeseries_engines()[self.engine] + # with engine.open(filters=filters) as ts: + # # test that the definitions file could be read properly + # self.assertGreaterEqual(len(ts.variables()), 2) + # + def test_api_reading_small_data_set(self): # test access to the EBAS API - engine = pyaro.list_timeseries_engines()["actrisebas"] - # sfilter = pyaro.timeseries.filters.get("stations", include=["Birkenes II"]) - with engine.open(vars_to_read="ozone mass concentration", filters=[], sites_to_read=["Birkenes II"]) as ts: - # test that the definitions file could be read properly - self.assertGreaterEqual((len(ts._def_data)['variables'], 2)) + filters = { + "variables": { + "include": [ + "ozone mass concentration", + ] + }, + "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + } + engine = pyaro.list_timeseries_engines()[self.engine] + # + with engine.open( + filters=filters, + ) as ts: + self.assertGreaterEqual(len(ts.variables()), 1) # def test_stationfilter(self): # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] From 647dd11d5a40e07c7dae9e853cac7ae790d07fc0 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:17:46 +0200 Subject: [PATCH 13/60] linting --- tests/test_ActrisEbasReader.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 87ea564..5c0ad89 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -9,6 +9,7 @@ TEST_URL = "https://prod-actris-md.nilu.no/Version" VOCABULARY_URL = "https://prod-actris-md.nilu.no/V" + class TestActrisEbasTimeSeriesReader(unittest.TestCase): engine = "actrisebas" From cb2217a91a7574b23a86c8ac28a83e19a528acc6 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:29:07 +0200 Subject: [PATCH 14/60] addjst to cached API response for CI --- .../actrisebas/ActrisEbasReader.py | 22 +- .../actrisebas/ozone mass concentration.json | 83768 ++++++++++++++++ 2 files changed, 83774 insertions(+), 16 deletions(-) create mode 100644 src/pyaro_readers/actrisebas/ozone mass concentration.json diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index a077fc3..54e4166 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -109,22 +109,12 @@ def __init__( self._def_data = self._read_definitions(file=DEFINITION_FILE) for var in vars_to_read: self._metadata[var] = {} - # for testing since the API is error-prone and slow - if test_flag: - test_file = os.path.join( - os.path.dirname(os.path.realpath(__file__)), - "..", - "..", - "..", - "tests", - "testdata", - "ACTRIS_EBAS", - f"{var}.json", - ) - if not os.path.exists(test_file): - raise ActrisEbasTestDataNotFoundException( - f"test file not found: {test_file}" - ) + # 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"{var}.json", + ) + if os.path.exists(test_file) and test_flag: with open(test_file, "r") as f: json_resp = json.load(f) else: 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. These measurements are gathered as a part of the following projects EMEP", + "title": "Ozone at Arkona", + "date_type": "creation", + "contact": [ + { + "first_name": "Yong", + "last_name": "Lin", + "organisation_name": "NILU", + "role_code": [ + "processor" + ], + "country_code": "NO", + "email": "ebas@nilu.no" + } + ], + "online_resource": { + "linkage": "https://ebas-data.nilu.no/" + }, + "identifier": { + "pid": "https://doi.org/10.48597/RTXS-U8P8", + "type": "DOI" + }, + "date": "2024-06-13T22:00:00.0000000Z" + }, + "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": ", EMEP, 1988-1989, Ozone at Arkona, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/RTXS-U8P8", + "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: EMEP." + }, + "md_keywords": { + "keywords": [ + "atmosphere", + "emep", + "gas phase", + "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": "suks", + "name": "Arkona", + "lat": 54.683333, + "lon": 13.433333, + "alt": 42.0, + "country_code": "DE", + "wmo_region": "Europe", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/suks" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 13.433333, + "east_bound_longitude": 13.433333, + "south_bound_latitude": 54.683333, + "north_bound_latitude": 54.683333 + }, + "ex_temporal_extent": { + "time_period_begin": "1987-12-31T23:00:00.0000000Z", + "time_period_end": "1989-12-30T23:00:00.0000000Z" + }, + "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/RT/XS/U8/RTXS-U8P8.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 670835.0 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/RT/XS/U8/RTXS-U8P8.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 670835.0 + } + ], + "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": [ + "EMEP" + ], + "variable_statistical_property": null, + "legacy_data": true, + "observation_timeliness": "scheduled", + "data_product": "full quality control", + "instrument_model": "Uv abs" + }, + "dq_data_quality_information": { + "compliance": "other" + }, + "provenance": { + "software": "https://git.nilu.no/ebas/ebas-io", + "version_history": null + } + }, + { + "md_metadata": { + "id": 203019, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "SGUS-M6X2.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-13T22:00:00.0000000Z", + "created": "2024-06-14T07:58:34.0000000Z", + "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 Ähtäri. These measurements are gathered as a part of the following projects EMEP", + "title": "Ozone at Ähtäri", + "date_type": "creation", + "contact": [ + { + "first_name": "Yong", + "last_name": "Lin", + "organisation_name": "NILU", + "role_code": [ + "processor" + ], + "country_code": "NO", + "email": "ebas@nilu.no" + } + ], + "online_resource": { + "linkage": "https://ebas-data.nilu.no/" + }, + "identifier": { + "pid": "https://doi.org/10.48597/SGUS-M6X2", + "type": "DOI" + }, + "date": "2024-06-13T22:00:00.0000000Z" + }, + "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": "Walden, J., EMEP, 1986-1997, Ozone at Ähtäri, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/SGUS-M6X2", + "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: EMEP." + }, + "md_keywords": { + "keywords": [ + "atmosphere", + "emep", + "gas phase", + "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": "w7qj", + "name": "Ähtäri", + "lat": 62.533333, + "lon": 24.221667, + "alt": 162.0, + "country_code": "FI", + "wmo_region": "Europe", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/w7qj" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 24.221667, + "east_bound_longitude": 24.221667, + "south_bound_latitude": 62.533333, + "north_bound_latitude": 62.533333 + }, + "ex_temporal_extent": { + "time_period_begin": "1986-08-30T22:00:00.0000000Z", + "time_period_end": "1997-05-28T22:00:00.0000000Z" + }, + "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/SG/US/M6/SGUS-M6X2.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 3459785.0 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/SG/US/M6/SGUS-M6X2.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 3459785.0 + } + ], + "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": [ + "EMEP" + ], + "variable_statistical_property": null, + "legacy_data": true, + "observation_timeliness": "scheduled", + "data_product": "full quality control", + "instrument_model": "Uv abs" + }, + "dq_data_quality_information": { + "compliance": "other" + }, + "provenance": { + "software": "https://git.nilu.no/ebas/ebas-io", + "version_history": null + } + }, + { + "md_metadata": { + "id": 203064, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "MDXS-DP46.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-13T22:00:00.0000000Z", + "created": "2024-06-14T07:59:18.0000000Z", + "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 La Tardière. 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These measurements are gathered as a part of the following projects GAW-WDCRG", + "title": "Ozone at Ryori", + "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/UVXT-DJDU", + "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, 2009-2024, Ozone at Ryori, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/UVXT-DJDU", + "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": "s93x", + "name": "Ryori", + "lat": 39.0319, + "lon": 141.8222, + "alt": 260.0, + "country_code": "JP", + "wmo_region": "Asia", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/s93x" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 141.8222, + "east_bound_longitude": 141.8222, + "south_bound_latitude": 39.0319, + "north_bound_latitude": 39.0319 + }, + "ex_temporal_extent": { + "time_period_begin": "2009-09-29T22:00:00.0000000Z", + "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/UV/XT/DJ/UVXT-DJDU.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 5612095.0 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/UV/XT/DJ/UVXT-DJDU.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 5612095.0 + } + ], + "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 + } + }, + { + "md_metadata": { + "id": 238755, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "6UMT-44C3.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-14T22:00:00.0000000Z", + "created": "2024-06-15T04:10:49.0000000Z", + "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 Minamitorishima. These measurements are gathered as a part of the following projects GAW-WDCRG", + "title": "Ozone at Minamitorishima", + "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/10.48597/6UMT-44C3", + "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, 2010-2024, Ozone at Minamitorishima, data hosted by EBAS at NILU, DOI: https://doi.org/10.48597/6UMT-44C3", + "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": "9jyd", + "name": "Minamitorishima", + "lat": 24.2883, + "lon": 153.9833, + "alt": 7.1, + "country_code": "JP", + "wmo_region": "Asia", + "identifier_type": "other PID", + "uri": "https://prod-actris-md.nilu.no/facilities/9jyd" + } + }, + "ex_geographic_bounding_box": { + "west_bound_longitude": 153.9833, + "east_bound_longitude": 153.9833, + "south_bound_latitude": 24.2883, + "north_bound_latitude": 24.2883 + }, + "ex_temporal_extent": { + "time_period_begin": "2010-05-30T22:00:00.0000000Z", + "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/6U/MT/44/6UMT-44C3.nc", + "protocol": "OPeNDAP", + "function": "streaming", + "restriction": { + "set": false + }, + "transfersize": 5602389.0 + }, + { + "data_format": "NETCDF", + "version_data_format": "4", + "dataset_url": "https://thredds.nilu.no/thredds/fileServer/ebas_doi/6U/MT/44/6UMT-44C3.nc", + "protocol": "HTTP", + "function": "download", + "restriction": { + "set": false + }, + "transfersize": 5602389.0 + } + ], + "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 + } + }, + { + "md_metadata": { + "id": 238757, + "provider": { + "name": "IN-SITU", + "atom": "http://localhost:5009/providers/14" + }, + "file_identifier": "EK83-VS9N.nc", + "language": "en", + "hierarchy_level": "dataset", + "online_resource": { + "linkage": "http://ebas.nilu.no/" + }, + "datestamp": "2024-06-14T22:00:00.0000000Z", + "created": "2024-06-15T04:10:53.0000000Z", + "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 Yonaguni. 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 From 42dc4eba992ec67be689b8c0806ce2a837fa7cee Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:36:14 +0200 Subject: [PATCH 15/60] include toml files --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 9f7b87d..b358b95 100644 --- a/setup.cfg +++ b/setup.cfg @@ -43,7 +43,7 @@ test_require = tox:tox where=src [options.package_data] -* = *.csv +* = *.csv, *.toml [options.entry_points] pyaro.timeseries = From c5b92a6e48358825c1bebad212dc5e97ebe314e2 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:41:23 +0200 Subject: [PATCH 16/60] add json file --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b358b95..3272878 100644 --- a/setup.cfg +++ b/setup.cfg @@ -43,7 +43,7 @@ test_require = tox:tox where=src [options.package_data] -* = *.csv, *.toml +* = *.csv, *.toml, *.json [options.entry_points] pyaro.timeseries = From 2dd3ff3e0f828e3f1f40f86e9cc2309f77971cc8 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 14:46:47 +0200 Subject: [PATCH 17/60] replace np.NAN with np.nan --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 54e4166..1b195cc 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -158,7 +158,7 @@ def read_data( lon = np.full(ts_no, tmp_data.attrs["geospatial_lon_min"]) station = np.full(ts_no, tmp_data.attrs["ebas_station_name"]) altitude = np.full(ts_no, tmp_data.attrs["geospatial_vertical_min"]) - standard_deviation = np.full(ts_no, np.NAN) + standard_deviation = np.full(ts_no, np.nan) # put all data variables in the data struct for the moment for _data_var in self._get_ebas_data_vars(tmp_data): From 52a873b663967ced0eb4e28be583cd2dad4c82e1 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 9 Sep 2024 16:41:26 +0200 Subject: [PATCH 18/60] WIP --- .../actrisebas/ActrisEbasReader.py | 49 +++++++++++++------ src/pyaro_readers/actrisebas/definitions.toml | 20 +++++++- tests/test_ActrisEbasReader.py | 38 +++++++------- 3 files changed, 70 insertions(+), 37 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 1b195cc..75a9e52 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -89,25 +89,25 @@ def __init__( ) try: - vars_to_read = filters["variables"]["include"] + self.vars_to_read = filters["variables"]["include"] except KeyError: raise ValueError( f"As of now, you have to give the species you want to read in filter.variables.include" ) try: - sites_to_read = filters["stations"]["include"] + self.sites_to_read = filters["stations"]["include"] except KeyError: - sites_to_read = [] + self.sites_to_read = [] try: - sites_to_exclude = filters["stations"]["exclude"] + self.sites_to_exclude = filters["stations"]["exclude"] except KeyError: - sites_to_exclude = [] + self.sites_to_exclude = [] # read config file self._def_data = self._read_definitions(file=DEFINITION_FILE) - for var in vars_to_read: + for var in self.vars_to_read: self._metadata[var] = {} # for testing since the API is error-prone and slow at the time of this writing test_file = os.path.join( @@ -129,8 +129,8 @@ def __init__( self._metadata[var] = json_resp self._urls_to_dl[var] = self.extract_urls( json_resp, - sites_to_read=sites_to_read, - sites_to_exclude=sites_to_exclude, + sites_to_read=self.sites_to_read, + sites_to_exclude=self.sites_to_exclude, ) self._data[var] = self.read_data(self._urls_to_dl[var]) @@ -141,7 +141,6 @@ def read_data( self, urls_to_dl: dict, tqdm_desc="reading stations", - sites_to_read: list[str] = None, ): """ read the data from EBAS thredds server @@ -150,7 +149,7 @@ def read_data( for s_idx, site_name in enumerate(urls_to_dl): for f_idx, url in enumerate(urls_to_dl[site_name]): tmp_data = xr.open_dataset(url) - # create times... + # 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) @@ -161,7 +160,16 @@ def read_data( standard_deviation = np.full(ts_no, np.nan) # put all data variables in the data struct for the moment - for _data_var in self._get_ebas_data_vars(tmp_data): + for d_idx, _data_var in enumerate( + self._get_ebas_data_vars( + tmp_data, + ) + ): + # the naming of the variable in the file does not reflect the vocabulary naming ot pyaerocom's + # naming + ret_data_var = _data_var.copy() + # if ret_data_var not in self.vars_to_read and : + # # we need vals = tmp_data[_data_var].values flags = np.full(ts_no, Flag.VALID) if _data_var not in self._data: @@ -181,6 +189,12 @@ def read_data( flag=flags, standard_deviation=standard_deviation, ) + # make sure to return something in the user given variable name for now + try: + if _data_var != self.vars_to_read[d_idx]: + self._data[self.vars_to_read[d_idx]] = self._data[_data_var] + except IndexError: + pass if not site_name in self._stations: self._stations[site_name] = Station( { @@ -219,7 +233,16 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non if len(tmp_data[data_var].dims) != 1: continue elif tmp_data[data_var].dims[0] in TIME_VAR_NAME: - data_vars.append(data_var) + # 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 @@ -292,9 +315,7 @@ class ActrisEbasTimeSeriesEngine(AutoFilterReaderEngine.AutoFilterEngine): def reader_class(self): return ActrisEbasTimeSeriesReader - # def open(self, filename, *args, **kwargs) -> ActrisEbasTimeSeriesReader: def open(self, *args, **kwargs) -> ActrisEbasTimeSeriesReader: - # return self.reader_class()(filename, *args, **kwargs) return self.reader_class()(*args, **kwargs) def description(self): diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index 36fe1d0..cf8383d 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -8,16 +8,32 @@ #ebas_component = [] #ebas_matrix = [] -[variables.vmro3] +[variables.conco3] actris_variable = ["ozone mass concentration", "ozone amount fraction"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] ebas_unit = "ug/m3" +[variables.vmro3] +actris_variable = ["ozone mass concentration", "ozone amount fraction"] +actris_matrix = ["gas phase"] +ebas_component = ["ozone"] +ebas_matrix = ["air"] +ebas_unit = "nmol/mol" + [variables.concso4] actris_variable = ["aerosol particle sulphate mass concentration"] actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] ebas_component = ["sulphate_corrected", "sulphate_total"] ebas_matrix = ["aerosol", "pm10", "pm25"] -ebas_unit = "ug/m3" \ No newline at end of file +ebas_unit = "ug/m3" + +[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 inb the first data file +"ozone mass concentration" = "nmol/mol" +"ozone amount fraction" = "nmol/mol" +"aerosol particle sulphate mass concentration" = "ug/m3" diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 5c0ad89..a63e426 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -64,17 +64,23 @@ def test_api_reading_small_data_set(self): ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) - # def test_stationfilter(self): - # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - # sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) - # with engine.open( - # self.file, filters=[sfilter], tqdm_desc="test_stationfilter" - # ) as ts: - # count = 0 - # for var in ts.variables(): - # count += len(ts.data(var)) - # self.assertEqual(count, 48775) - # self.assertEqual(len(ts.stations()), 3) + def test_api_reading_pyaerocom_naming(self): + # test access to the EBAS API + filters = { + "variables": { + "include": [ + "vmro3", + ] + }, + "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + } + engine = pyaro.list_timeseries_engines()[self.engine] + # + with engine.open( + filters=filters, + ) as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + # # def test_wrappers(self): # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] @@ -85,16 +91,6 @@ def test_api_reading_small_data_set(self): # self.assertEqual(ts.data(new_var_name).variable, new_var_name) # pass # - # def test_variables_filter(self): - # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - # new_var_name = "od550aer" - # vfilter = pyaro.timeseries.filters.get( - # "variables", reader_to_new={"AOD_550nm": new_var_name} - # ) - # with engine.open( - # self.file, filters=[vfilter], tqdm_desc="test_variables_filter" - # ) as ts: - # self.assertEqual(ts.data(new_var_name).variable, new_var_name) if __name__ == "__main__": From a900ef63301f587c286731d03adc377903c21e9b Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 10 Sep 2024 14:39:35 +0200 Subject: [PATCH 19/60] WIP --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 16 ++++++---------- tests/test_ActrisEbasReader.py | 2 -- 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 75a9e52..8196c21 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -1,15 +1,12 @@ +import datetime +import json import logging +import os import tomllib -from io import BytesIO from urllib.parse import urlparse, quote -from urllib.request import urlopen - -from urllib3.util.retry import Retry -from urllib3.poolmanager import PoolManager import numpy as np -import requests -import json +import xarray as xr from pyaro.timeseries import ( AutoFilterReaderEngine, Data, @@ -18,9 +15,8 @@ Station, ) from tqdm import tqdm -import datetime -import xarray as xr -import os +from urllib3.poolmanager import PoolManager +from urllib3.util.retry import Retry logger = logging.getLogger(__name__) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index a63e426..da585e9 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -1,10 +1,8 @@ import unittest import urllib.request -import os 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" From 4a7b795e81a27dca1d5a640c38e1885c2fddfca1 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 10 Sep 2024 16:37:53 +0200 Subject: [PATCH 20/60] linting --- setup.cfg | 2 +- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 3272878..834f80b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -64,7 +64,7 @@ min_version = 4.0 skip_missing_interpreters = True isolated_build = True env_list = - py310 + py311 format #depends = diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 8196c21..02a695c 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -145,13 +145,14 @@ def read_data( for s_idx, site_name in enumerate(urls_to_dl): for f_idx, url in enumerate(urls_to_dl[site_name]): tmp_data = xr.open_dataset(url) + long_name = tmp_data.attrs["ebas_station_name"] # 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_name"]) + station = np.full(ts_no, tmp_data.attrs["ebas_station_code"]) altitude = np.full(ts_no, tmp_data.attrs["geospatial_vertical_min"]) standard_deviation = np.full(ts_no, np.nan) From d1408023caa20492b8098183b71052e93076c7b3 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 10 Sep 2024 16:47:27 +0200 Subject: [PATCH 21/60] linting --- .../actrisebas/ActrisEbasReader.py | 40 +++++++++---------- tests/test_ActrisEbasReader.py | 4 +- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 02a695c..1fd30e9 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -64,11 +64,11 @@ class ActrisEbasTestDataNotFoundException(Exception): class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( - self, - filters=[], - tqdm_desc: str | None = None, - ts_type: str = "daily", - test_flag: bool = True, + self, + filters=[], + tqdm_desc: str | None = None, + ts_type: str = "daily", + test_flag: bool = True, ): """ """ self._filename = None @@ -134,9 +134,9 @@ def metadata(self): return self._metadata def read_data( - self, - urls_to_dl: dict, - tqdm_desc="reading stations", + self, + urls_to_dl: dict, + tqdm_desc="reading stations", ): """ read the data from EBAS thredds server @@ -158,9 +158,9 @@ def read_data( # 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, - ) + self._get_ebas_data_vars( + tmp_data, + ) ): # the naming of the variable in the file does not reflect the vocabulary naming ot pyaerocom's # naming @@ -234,8 +234,8 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non try: # if defined, return only names that match if ( - tmp_data[data_var].attrs["units"] - == self._def_data["actris_std_units"][data_var] + tmp_data[data_var].attrs["units"] + == self._def_data["actris_std_units"][data_var] ): data_vars.append(data_var) except KeyError: @@ -244,10 +244,10 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non return data_vars def extract_urls( - self, - json_resp: dict, - sites_to_read: list[str] = [], - sites_to_exclude: list[str] = [], + 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 @@ -267,11 +267,11 @@ def extract_urls( # 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] + site_data[DISTRIBUTION_ROOT_KEY] ): if ( - distribution_data[DISTRIBUTION_PROTOCOL_KEY] - != DISTRIBUTION_PROTOCOL_NAME + distribution_data[DISTRIBUTION_PROTOCOL_KEY] + != DISTRIBUTION_PROTOCOL_NAME ): continue else: diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index da585e9..231aee0 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -58,7 +58,7 @@ def test_api_reading_small_data_set(self): engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, + filters=filters, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) @@ -75,7 +75,7 @@ def test_api_reading_pyaerocom_naming(self): engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, + filters=filters, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) From 0692e97f055019fa556f6e30fb3735c8d81717fd Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Wed, 11 Sep 2024 14:59:42 +0200 Subject: [PATCH 22/60] WIP: potential filtering problem with pyaro --- .../actrisebas/ActrisEbasReader.py | 105 ++++++++++++++---- src/pyaro_readers/actrisebas/definitions.toml | 14 ++- tests/test_ActrisEbasReader.py | 33 +++--- 3 files changed, 117 insertions(+), 35 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 1fd30e9..c4da33b 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -31,6 +31,8 @@ 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 @@ -54,10 +56,19 @@ TIME_VAR_NAME = ["time"] + class ActrisEbasRetryException(Exception): pass +class ActrisEbasStdNameNotFoundException(Exception): + pass + + +class ActrisEbasQcVariableNotFoundException(Exception): + pass + + class ActrisEbasTestDataNotFoundException(Exception): pass @@ -65,6 +76,7 @@ class ActrisEbasTestDataNotFoundException(Exception): class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, + vars_to_read: list[str] = None, filters=[], tqdm_desc: str | None = None, ts_type: str = "daily", @@ -72,24 +84,30 @@ def __init__( ): """ """ self._filename = None + 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 = {} + self._standard_names = {} _laststatstr = "" - self._revision = datetime.datetime.min + self._revision = datetime.datetime.now() self._metadata["revision"] = datetime.datetime.strftime( self._revision, "%y%m%d%H%M%S" ) - try: - self.vars_to_read = filters["variables"]["include"] - except KeyError: - raise ValueError( - f"As of now, you have to give the species you want to read in filter.variables.include" - ) + 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}...") + # try: + # self.vars_to_read = filters["variables"]["include"] + # except KeyError: + # raise ValueError( + # f"As of now, you have to give the species you want to read in filter.variables.include" + # ) try: self.sites_to_read = filters["stations"]["include"] @@ -105,6 +123,7 @@ def __init__( self._def_data = self._read_definitions(file=DEFINITION_FILE) for var in self.vars_to_read: self._metadata[var] = {} + self._standard_names[var] = self.get_actris_standard_name(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__)), @@ -128,13 +147,15 @@ def __init__( sites_to_read=self.sites_to_read, sites_to_exclude=self.sites_to_exclude, ) - self._data[var] = self.read_data(self._urls_to_dl[var]) + self.read_data(var, self._urls_to_dl[var]) + # assert self.data(self.vars_to_read[0]) def metadata(self): return self._metadata def read_data( self, + actris_variable: str, urls_to_dl: dict, tqdm_desc="reading stations", ): @@ -164,17 +185,25 @@ def read_data( ): # the naming of the variable in the file does not reflect the vocabulary naming ot pyaerocom's # naming - ret_data_var = _data_var.copy() + # ret_data_var = _data_var.copy() # if ret_data_var not in self.vars_to_read and : # # we need + + # look for a standard_name match and return only that variable + std_name = self._standard_names[actris_variable] + if self.get_ebas_data_standard_name(tmp_data, _data_var) != self._standard_names[actris_variable]: + logger.info(f"file #{d_idx: }skipping variable {_data_var} due to wrong standard name") + print(f"file #{d_idx: } skipping variable {_data_var} due to wrong standard name") + continue + vals = tmp_data[_data_var].values flags = np.full(ts_no, Flag.VALID) - if _data_var not in self._data: - self._data[_data_var] = NpStructuredData( - _data_var, self.get_ebas_data_units(tmp_data, _data_var) + if actris_variable not in self._data: + self._data[actris_variable] = NpStructuredData( + actris_variable, self.get_ebas_data_units(tmp_data, _data_var) ) - self._data[_data_var].append( + self._data[actris_variable].append( value=vals, station=station, latitude=lat, @@ -187,11 +216,11 @@ def read_data( standard_deviation=standard_deviation, ) # make sure to return something in the user given variable name for now - try: - if _data_var != self.vars_to_read[d_idx]: - self._data[self.vars_to_read[d_idx]] = self._data[_data_var] - except IndexError: - pass + # try: + # if _data_var != self.vars_to_read[d_idx]: + # self._data[self.vars_to_read[d_idx]] = self._data[_data_var] + # except IndexError: + # pass if not site_name in self._stations: self._stations[site_name] = Station( { @@ -201,7 +230,7 @@ def read_data( "altitude": altitude[0], "country": self.get_ebas_data_country_code(tmp_data), "url": "", - "long_name": site_name, + "long_name": long_name, } ) bar.update(1) @@ -212,10 +241,48 @@ def get_ebas_data_units(self, tmp_data, var_name): 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 = tmp_data[var_name].attrs["standard_name"] + 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"] + 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: + ret_data = var_name + break + if ret_data is None: + raise ActrisEbasQcVariableNotFoundException(f"Error: no flag data for variable {var_name} found!") + return ret_data + 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 diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index cf8383d..231e82d 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -9,11 +9,12 @@ #ebas_matrix = [] [variables.conco3] -actris_variable = ["ozone mass concentration", "ozone amount fraction"] +actris_variable = ["ozone mass concentration"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] ebas_unit = "ug/m3" +standard_name = "mass_concentration_of_ozone_in_air" [variables.vmro3] actris_variable = ["ozone mass concentration", "ozone amount fraction"] @@ -21,6 +22,7 @@ actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] ebas_unit = "nmol/mol" +standard_name = "mole_fraction_of_ozone_in_air" [variables.concso4] actris_variable = ["aerosol particle sulphate mass concentration"] @@ -28,12 +30,20 @@ actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] ebas_component = ["sulphate_corrected", "sulphate_total"] ebas_matrix = ["aerosol", "pm10", "pm25"] ebas_unit = "ug/m3" +standard_name = "mass_concentration_of_sulfate_aerosol_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 inb the first data file -"ozone mass concentration" = "nmol/mol" +"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 +"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_sulfate_aerosol_in_air" diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 231aee0..ac3cabe 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -3,6 +3,7 @@ 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" @@ -11,6 +12,11 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): engine = "actrisebas" + station_filter = { + "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + } + vars_to_read = ["ozone mass concentration"] + def test_api_online(self, url=TEST_URL): try: req = urllib.request.Request(TEST_URL, method="HEAD") @@ -48,19 +54,16 @@ def test_init(self): def test_api_reading_small_data_set(self): # test access to the EBAS API filters = { - "variables": { - "include": [ - "ozone mass concentration", - ] - }, "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, } engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, + filters=filters, vars_to_read=["ozone mass concentration"], ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) + self.assertEqual(len(ts.stations()), 2) + self.assertIn("revision", ts.metadata()) def test_api_reading_pyaerocom_naming(self): # test access to the EBAS API @@ -76,18 +79,20 @@ def test_api_reading_pyaerocom_naming(self): # with engine.open( filters=filters, + vars_to_read=["vmro3"], ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) # - # def test_wrappers(self): - # engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - # new_var_name = "od500aer" - # with VariableNameChangingReader( - # engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} - # ) as ts: - # self.assertEqual(ts.data(new_var_name).variable, new_var_name) - # pass + def test_wrappers(self): + engine = pyaro.list_timeseries_engines()[self.engine] + new_var_name = "vmro3" + with VariableNameChangingReader( + engine.open(vars_to_read=self.vars_to_read, filters=self.station_filter), + {self.vars_to_read[0]: new_var_name} + ) as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + pass # From c164d677e79b42a61f7816a2324835e10117fde6 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 17 Sep 2024 11:26:49 +0200 Subject: [PATCH 23/60] WIP: ozone reading working --- .../actrisebas/ActrisEbasReader.py | 39 +++++++---- tests/test_ActrisEbasReader.py | 65 ++++++++++--------- 2 files changed, 63 insertions(+), 41 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index c4da33b..1a14b2d 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -3,6 +3,7 @@ import logging import os import tomllib +from copy import deepcopy from urllib.parse import urlparse, quote import numpy as np @@ -56,7 +57,6 @@ TIME_VAR_NAME = ["time"] - class ActrisEbasRetryException(Exception): pass @@ -148,7 +148,7 @@ def __init__( sites_to_exclude=self.sites_to_exclude, ) self.read_data(var, self._urls_to_dl[var]) - # assert self.data(self.vars_to_read[0]) + assert self._data[self.vars_to_read[0]] def metadata(self): return self._metadata @@ -167,13 +167,15 @@ def read_data( for f_idx, url in enumerate(urls_to_dl[site_name]): tmp_data = xr.open_dataset(url) 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, 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) @@ -190,17 +192,24 @@ def read_data( # # we need # look for a standard_name match and return only that variable - std_name = self._standard_names[actris_variable] - if self.get_ebas_data_standard_name(tmp_data, _data_var) != self._standard_names[actris_variable]: - logger.info(f"file #{d_idx: }skipping variable {_data_var} due to wrong standard name") - print(f"file #{d_idx: } skipping variable {_data_var} due to wrong standard name") + if ( + self.get_ebas_data_standard_name(tmp_data, _data_var) + != self._standard_names[actris_variable] + ): + logger.info( + f"station {site_name}, file #{f_idx}: skipping variable {_data_var} due to wrong standard name" + ) + print( + f"station {site_name},file #{f_idx}: skipping variable {_data_var} due to wrong standard name" + ) continue vals = tmp_data[_data_var].values flags = np.full(ts_no, Flag.VALID) if actris_variable not in self._data: self._data[actris_variable] = NpStructuredData( - actris_variable, self.get_ebas_data_units(tmp_data, _data_var) + actris_variable, + self.get_ebas_data_units(tmp_data, _data_var), ) self._data[actris_variable].append( @@ -230,7 +239,7 @@ def read_data( "altitude": altitude[0], "country": self.get_ebas_data_country_code(tmp_data), "url": "", - "long_name": long_name, + "long_name": stat_code, } ) bar.update(1) @@ -269,7 +278,9 @@ def get_ebas_data_qc_variable(self, tmp_data, var_name): ret_data = var_name break if ret_data is None: - raise ActrisEbasQcVariableNotFoundException(f"Error: no flag data for variable {var_name} found!") + raise ActrisEbasQcVariableNotFoundException( + f"Error: no flag data for variable {var_name} found!" + ) return ret_data def get_ebas_data_country_code(self, tmp_data): @@ -281,7 +292,9 @@ def get_actris_standard_name(self, actris_var_name): 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!") + 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): """ @@ -349,7 +362,9 @@ def extract_urls( return urls_to_dl def _unfiltered_data(self, varname) -> Data: - return self._data[varname] + ret_data = deepcopy(self._data[varname]) + return ret_data + # return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: return self._stations diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index ac3cabe..1813374 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -55,45 +55,52 @@ def test_api_reading_small_data_set(self): # test access to the EBAS API filters = { "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + # "variables": { + # "include": self.vars_to_read, + # }, } engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, vars_to_read=["ozone mass concentration"], + filters=filters, + vars_to_read=self.vars_to_read, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) self.assertEqual(len(ts.stations()), 2) - self.assertIn("revision", ts.metadata()) + self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) - def test_api_reading_pyaerocom_naming(self): - # test access to the EBAS API - filters = { - "variables": { - "include": [ - "vmro3", - ] - }, - "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - } - engine = pyaro.list_timeseries_engines()[self.engine] - # - with engine.open( - filters=filters, - vars_to_read=["vmro3"], - ) as ts: - self.assertGreaterEqual(len(ts.variables()), 1) + self.assertIn("revision", ts.metadata()) + # def test_api_reading_pyaerocom_naming(self): + # # test access to the EBAS API + # filters = { + # "variables": { + # "include": [ + # "vmro3", + # ] + # }, + # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + # } + # engine = pyaro.list_timeseries_engines()[self.engine] + # # + # with engine.open( + # filters=filters, + # vars_to_read=["vmro3"], + # ) as ts: + # self.assertGreaterEqual(len(ts.variables()), 1) # - def test_wrappers(self): - engine = pyaro.list_timeseries_engines()[self.engine] - new_var_name = "vmro3" - with VariableNameChangingReader( - engine.open(vars_to_read=self.vars_to_read, filters=self.station_filter), - {self.vars_to_read[0]: new_var_name} - ) as ts: - self.assertEqual(ts.data(new_var_name).variable, new_var_name) - pass - # + # # + # def test_wrappers(self): + # engine = pyaro.list_timeseries_engines()[self.engine] + # new_var_name = "vmro3" + # with VariableNameChangingReader( + # engine.open(vars_to_read=self.vars_to_read, filters=self.station_filter), + # {self.vars_to_read[0]: new_var_name} + # ) as ts: + # self.assertEqual(ts.data(new_var_name).variable, new_var_name) + # pass + # # if __name__ == "__main__": From 42c905b361bb83377daf7352d0a153898c43e825 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 17 Sep 2024 14:20:52 +0200 Subject: [PATCH 24/60] WIP: ozone reading with pyaerocom variable name working --- src/pyaro_readers/actrisebas/definitions.toml | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index 231e82d..bcf01e2 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -13,33 +13,27 @@ actris_variable = ["ozone mass concentration"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] -ebas_unit = "ug/m3" -standard_name = "mass_concentration_of_ozone_in_air" [variables.vmro3] -actris_variable = ["ozone mass concentration", "ozone amount fraction"] +actris_variable = ["ozone amount fraction"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] -ebas_unit = "nmol/mol" -standard_name = "mole_fraction_of_ozone_in_air" [variables.concso4] actris_variable = ["aerosol particle sulphate mass concentration"] actris_matrix = ["aerosol particle phase", "PM10", "PM2.5"] ebas_component = ["sulphate_corrected", "sulphate_total"] ebas_matrix = ["aerosol", "pm10", "pm25"] -ebas_unit = "ug/m3" -standard_name = "mass_concentration_of_sulfate_aerosol_in_air" -[actris_std_units] +#[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 inb the first data file -"ozone mass concentration" = "ug/m3" -"ozone amount fraction" = "nmol/mol" -"aerosol particle sulphate mass concentration" = "ug/m3" +# 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 From 316171b5f55a5665bec63b91cfa591f55502558d Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 17 Sep 2024 14:21:02 +0200 Subject: [PATCH 25/60] WIP: ozone reading with pyaerocom variable name working --- .../actrisebas/ActrisEbasReader.py | 126 +++++++++++------- tests/test_ActrisEbasReader.py | 38 +++--- 2 files changed, 99 insertions(+), 65 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 1a14b2d..4fead46 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -25,7 +25,7 @@ # BASE_API_URL = "https://prod-actris-md.nilu.no/Vocabulary/categories" 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/" +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" @@ -89,26 +89,25 @@ def __init__( self._urls_to_dl = {} self._data = {} # var -> {data-array} self._set_filters(filters) - self._header = [] + # 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 = "" + # _laststatstr = "" self._revision = datetime.datetime.now() self._metadata["revision"] = datetime.datetime.strftime( self._revision, "%y%m%d%H%M%S" ) - 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}...") - # try: - # self.vars_to_read = filters["variables"]["include"] - # except KeyError: - # raise ValueError( - # f"As of now, you have to give the species you want to read in filter.variables.include" - # ) + # 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: @@ -121,34 +120,73 @@ def __init__( # 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] = {} - self._standard_names[var] = self.get_actris_standard_name(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"{var}.json", - ) - if os.path.exists(test_file) and test_flag: - with open(test_file, "r") as f: - json_resp = json.load(f) + # 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"]: + # use 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: - # search for variable metadata - query_url = f"{VAR_QUERY_URL}{quote(var)}" - retries = Retry(connect=5, read=2, redirect=5) - http = PoolManager(retries=retries) - response = http.request("GET", query_url) - - json_resp = json.loads(response.data.decode("utf-8")) - - self._metadata[var] = json_resp - self._urls_to_dl[var] = self.extract_urls( - json_resp, - sites_to_read=self.sites_to_read, - sites_to_exclude=self.sites_to_exclude, - ) - self.read_data(var, self._urls_to_dl[var]) - assert self._data[self.vars_to_read[0]] + # 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: + # search for variable metadata + query_url = ( + f"{VAR_QUERY_URL}{quote(self._actris_vars_to_read[_pyaro_var])}" + ) + retries = Retry(connect=5, read=2, redirect=5) + http = PoolManager(retries=retries) + response = http.request("GET", query_url) + json_resp = json.loads(response.data.decode("utf-8")) + + 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] def metadata(self): return self._metadata @@ -185,16 +223,10 @@ def read_data( tmp_data, ) ): - # the naming of the variable in the file does not reflect the vocabulary naming ot pyaerocom's - # naming - # ret_data_var = _data_var.copy() - # if ret_data_var not in self.vars_to_read and : - # # we need - # look for a standard_name match and return only that variable if ( self.get_ebas_data_standard_name(tmp_data, _data_var) - != self._standard_names[actris_variable] + 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" @@ -362,9 +394,7 @@ def extract_urls( return urls_to_dl def _unfiltered_data(self, varname) -> Data: - ret_data = deepcopy(self._data[varname]) - return ret_data - # return self._data[varname] + return self._data[varname] def _unfiltered_stations(self) -> dict[str, Station]: return self._stations diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 1813374..394ca78 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -16,6 +16,7 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, } vars_to_read = ["ozone mass concentration"] + pyaerocom_vars_to_read = ["conco3"] def test_api_online(self, url=TEST_URL): try: @@ -72,23 +73,26 @@ def test_api_reading_small_data_set(self): self.assertIn("revision", ts.metadata()) - # def test_api_reading_pyaerocom_naming(self): - # # test access to the EBAS API - # filters = { - # "variables": { - # "include": [ - # "vmro3", - # ] - # }, - # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - # } - # engine = pyaro.list_timeseries_engines()[self.engine] - # # - # with engine.open( - # filters=filters, - # vars_to_read=["vmro3"], - # ) as ts: - # self.assertGreaterEqual(len(ts.variables()), 1) + def test_api_reading_pyaerocom_naming(self): + # test access to the EBAS API + filters = { + "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + # "variables": { + # "include": self.vars_to_read, + # }, + } + engine = pyaro.list_timeseries_engines()[self.engine] + # + with engine.open( + filters=filters, + vars_to_read=self.pyaerocom_vars_to_read, + test_flag=True, + ) as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) + # # # # def test_wrappers(self): From 2f6bcaf4d05ac668b4bdef1bf56649329bead72c Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 17 Sep 2024 14:39:04 +0200 Subject: [PATCH 26/60] linting --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 8 ++++---- tests/test_ActrisEbasReader.py | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 4fead46..d008909 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -76,7 +76,7 @@ class ActrisEbasTestDataNotFoundException(Exception): class ActrisEbasTimeSeriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( self, - vars_to_read: list[str] = None, + vars_to_read: list[str] = None, filters=[], tqdm_desc: str | None = None, ts_type: str = "daily", @@ -193,7 +193,7 @@ def metadata(self): def read_data( self, - actris_variable: str, + actris_variable: str, urls_to_dl: dict, tqdm_desc="reading stations", ): @@ -225,8 +225,8 @@ def read_data( ): # look for a standard_name match and return only that variable if ( - self.get_ebas_data_standard_name(tmp_data, _data_var) - not in self._standard_names[actris_variable] + self.get_ebas_data_standard_name(tmp_data, _data_var) + 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" diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 394ca78..9c5caff 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -63,8 +63,8 @@ def test_api_reading_small_data_set(self): engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, - vars_to_read=self.vars_to_read, + filters=filters, + vars_to_read=self.vars_to_read, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) self.assertEqual(len(ts.stations()), 2) @@ -84,9 +84,9 @@ def test_api_reading_pyaerocom_naming(self): engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, - vars_to_read=self.pyaerocom_vars_to_read, - test_flag=True, + filters=filters, + vars_to_read=self.pyaerocom_vars_to_read, + test_flag=True, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) self.assertEqual(len(ts.stations()), 2) From 8a0a41abfc5ab53fb06625016e8b01eb37004159 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 17 Sep 2024 16:54:24 +0200 Subject: [PATCH 27/60] WIP: started applying flags --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index d008909..10b5cde 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -237,6 +237,9 @@ def read_data( continue 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 actris_variable not in self._data: self._data[actris_variable] = NpStructuredData( @@ -293,7 +296,7 @@ def get_ebas_data_ancillary_variables(self, tmp_data, var_name): 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"] + ret_data = tmp_data[var_name].attrs["ancillary_variables"].split() return ret_data def get_ebas_data_qc_variable(self, tmp_data, var_name): @@ -307,13 +310,12 @@ def get_ebas_data_qc_variable(self, tmp_data, var_name): 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: - ret_data = var_name - break + return var if ret_data is None: raise ActrisEbasQcVariableNotFoundException( f"Error: no flag data for variable {var_name} found!" ) - return ret_data + return "" def get_ebas_data_country_code(self, tmp_data): """small helper method to get the ebas country code from the data file""" From e763f2cf4ea1b579379eb3eb385a7dfc896e7f4f Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 14:10:57 +0200 Subject: [PATCH 28/60] use paginated API --- .../actrisebas/ActrisEbasReader.py | 54 ++++++++++++++----- tests/test_ActrisEbasReader.py | 9 ++++ 2 files changed, 49 insertions(+), 14 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 10b5cde..bb5e781 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -3,11 +3,16 @@ import logging import os import tomllib -from copy import deepcopy + 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, @@ -15,19 +20,18 @@ NpStructuredData, Station, ) -from tqdm import tqdm -from urllib3.poolmanager import PoolManager -from urllib3.util.retry import Retry logger = logging.getLogger(__name__) # default API URL base # BASE_API_URL = "https://prod-actris-md.nilu.no/Vocabulary/categories" -BASE_API_URL = "https://prod-actris-md.nilu.no/" +BASE_API_URL = "https://dev-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 @@ -80,7 +84,7 @@ def __init__( filters=[], tqdm_desc: str | None = None, ts_type: str = "daily", - test_flag: bool = True, + test_flag: bool = False, ): """ """ self._filename = None @@ -101,6 +105,7 @@ def __init__( 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"]: @@ -165,14 +170,19 @@ def __init__( with open(test_file, "r") as f: json_resp = json.load(f) else: - # search for variable metadata - query_url = ( - f"{VAR_QUERY_URL}{quote(self._actris_vars_to_read[_pyaro_var])}" - ) - retries = Retry(connect=5, read=2, redirect=5) - http = PoolManager(retries=retries) - response = http.request("GET", query_url) - json_resp = json.loads(response.data.decode("utf-8")) + 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}" + print(query_url) + retries = Retry(connect=5, read=2, redirect=5) + http = PoolManager(retries=retries) + response = http.request("GET", query_url) + json_resp_tmp = json.loads(response.data.decode("utf-8")) + json_resp.extend(json_resp_tmp) + page_no += 1 self._metadata[_pyaro_var][_actris_var] = json_resp self._urls_to_dl[_actris_var] = self.extract_urls( @@ -280,6 +290,22 @@ def read_data( bar.update(1) bar.close() + 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 valis 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"] diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 9c5caff..25519bc 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -17,6 +17,7 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): } vars_to_read = ["ozone mass concentration"] pyaerocom_vars_to_read = ["conco3"] + # pyaerocom_vars_to_read = ["vmro3"] def test_api_online(self, url=TEST_URL): try: @@ -44,6 +45,14 @@ def test_init(self): 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(self): # # test access to the EBAS API # filters={"variables": {"include": ["ozone mass concentration", ]}} From d29b0372b3e79c41fbd1ba65218572d31e86cb7a Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 14:20:18 +0200 Subject: [PATCH 29/60] adjusted logging --- .../actrisebas/ActrisEbasReader.py | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index bb5e781..1a4cff7 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -9,6 +9,7 @@ import numpy as np import polars import xarray as xr +from gpxpy.gpx import var_name from tqdm import tqdm from urllib3.poolmanager import PoolManager from urllib3.util.retry import Retry @@ -176,7 +177,7 @@ def __init__( 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}" - print(query_url) + logger.info(query_url) retries = Retry(connect=5, read=2, redirect=5) http = PoolManager(retries=retries) response = http.request("GET", query_url) @@ -234,17 +235,16 @@ def read_data( ) ): # look for a standard_name match and return only that variable - if ( - self.get_ebas_data_standard_name(tmp_data, _data_var) - not in self._standard_names[actris_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: logger.info( - f"station {site_name}, file #{f_idx}: skipping variable {_data_var} due to wrong standard name" - ) - print( - f"station {site_name},file #{f_idx}: skipping variable {_data_var} due to wrong standard name" + f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" ) - continue vals = tmp_data[_data_var].values # apply flags From c018de191bac2cd4c7f87cccf76779c704bb025f Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 14:50:15 +0200 Subject: [PATCH 30/60] bum version --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 834f80b..0204dfd 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.10.dev2 +version = 0.0.10.dev3 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md @@ -54,8 +54,8 @@ pyaro.timeseries = netcdf_rw = pyaro_readers.netcdf_rw:Netcdf_RWTimeseriesEngine harp = pyaro_readers.harpreader:AeronetHARPEngine nilupmfabsorption = pyaro_readers.nilupmfabsorptionreader:NILUPMFAbsorptionTimeseriesEngine - nilupmfebas = pyaro_readers.nilupmfebas:EbasPmfTimeseriesEngine actrisebas = pyaro_readers.actrisebas:ActrisEbasTimeSeriesEngine + nilupmfebas = pyaro_readers.nilupmfebas:EbasPmfTimeseriesEngine From 787619c35c397531ab0a5f5d48e81e2d60ffd422 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 14:51:42 +0200 Subject: [PATCH 31/60] bump pyaro version --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 0204dfd..d331423 100644 --- a/setup.cfg +++ b/setup.cfg @@ -21,7 +21,7 @@ url = https://github.com/metno/pyaro-readers [options] python_version = >=3.10 install_requires = - pyaro >= 0.0.10 + pyaro >= 0.0.12 geocoder_reverse_natural_earth >= 0.0.2 netCDF4 requests From b926de99089682b1fcab3c991201f36043416dfe Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 14:57:31 +0200 Subject: [PATCH 32/60] correct pyaro version --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d331423..bc535cc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -21,7 +21,7 @@ url = https://github.com/metno/pyaro-readers [options] python_version = >=3.10 install_requires = - pyaro >= 0.0.12 + pyaro >= 0.0.11 geocoder_reverse_natural_earth >= 0.0.2 netCDF4 requests From b39fdbd7b42ec3edaa7dbb77e775ecc44fd706e6 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 15:00:52 +0200 Subject: [PATCH 33/60] WIP --- .github/workflows/CI.yml | 2 +- setup.cfg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 9aa24c7..77bac7d 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -8,7 +8,7 @@ jobs: lint: runs-on: ubuntu-latest env: - PYTHON: 3.9 + PYTHON: 3.11 steps: - uses: actions/checkout@v3 with: diff --git a/setup.cfg b/setup.cfg index bc535cc..0204dfd 100644 --- a/setup.cfg +++ b/setup.cfg @@ -21,7 +21,7 @@ url = https://github.com/metno/pyaro-readers [options] python_version = >=3.10 install_requires = - pyaro >= 0.0.11 + pyaro >= 0.0.10 geocoder_reverse_natural_earth >= 0.0.2 netCDF4 requests From f10bdb3a0b5bf706f06fb2e9e134c82f511ccc92 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 15:11:13 +0200 Subject: [PATCH 34/60] test updated CI.yml --- .github/workflows/CI.yml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 77bac7d..a8c7132 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: 3.11 + 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 3.11 + uses: actions/setup-python@v5 with: - python-version: ${{ env.PYTHON }} + python-version: "3.11" - 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 From 284ac3bcf05262018347af2463968fe22ae67ff9 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 15:15:38 +0200 Subject: [PATCH 35/60] optimised imports --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 1a4cff7..18bb297 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -9,7 +9,6 @@ import numpy as np import polars import xarray as xr -from gpxpy.gpx import var_name from tqdm import tqdm from urllib3.poolmanager import PoolManager from urllib3.util.retry import Retry From 4305ce61756da04fc34687dad4dfb4f8b4b77cba Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 19 Sep 2024 15:20:25 +0200 Subject: [PATCH 36/60] linting with Pytyhon 3.10 --- .github/workflows/CI.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index a8c7132..fa7118b 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -12,10 +12,10 @@ jobs: - uses: actions/checkout@v4 with: lfs: 'true' - - name: Set up Python 3.11 + - name: Set up Python 3.10 uses: actions/setup-python@v5 with: - python-version: "3.11" + python-version: "3.10" - name: Python info run: | which python From f66f699800dd27b5bc8b736defe03523cdf53ccf Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 20 Sep 2024 16:29:57 +0200 Subject: [PATCH 37/60] WIP getting pyaerocom variable concso4t to work properly --- .../actrisebas/ActrisEbasReader.py | 59 ++++++++++--------- src/pyaro_readers/actrisebas/definitions.toml | 31 ++++++++-- tests/test_ActrisEbasReader.py | 39 +++++++----- 3 files changed, 80 insertions(+), 49 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 18bb297..86a26b2 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -115,12 +115,12 @@ def __init__( # read only stations according to the station filter try: self.sites_to_read = filters["stations"]["include"] - except KeyError: + except (KeyError, TypeError) as e: self.sites_to_read = [] try: self.sites_to_exclude = filters["stations"]["exclude"] - except KeyError: + except (KeyError, TypeError) as e: self.sites_to_exclude = [] # read config file @@ -147,12 +147,13 @@ def __init__( 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) - ] + 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) @@ -210,22 +211,10 @@ def read_data( """ read the data from EBAS thredds server """ - bar = tqdm(desc=tqdm_desc, total=len(urls_to_dl)) + 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]): tmp_data = xr.open_dataset(url) - 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) # put all data variables in the data struct for the moment for d_idx, _data_var in enumerate( @@ -241,10 +230,24 @@ def read_data( # ) continue else: + bla = f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" logger.info( f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" ) + 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) @@ -268,12 +271,8 @@ def read_data( flag=flags, standard_deviation=standard_deviation, ) - # make sure to return something in the user given variable name for now - # try: - # if _data_var != self.vars_to_read[d_idx]: - # self._data[self.vars_to_read[d_idx]] = self._data[_data_var] - # except IndexError: - # pass + # stop after the 1st matching variable + break if not site_name in self._stations: self._stations[site_name] = Station( { @@ -312,7 +311,11 @@ def get_ebas_data_units(self, tmp_data, var_name): 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 = tmp_data[var_name].attrs["standard_name"] + 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): diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index bcf01e2..ea116cf 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -13,18 +13,33 @@ 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_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] +standard_names = ["mole_fraction_of_ozone_in_air"] -[variables.concso4] + +[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", "sulphate_total"] +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", ] #[actris_std_units] # tell the reader which unit shall be returned in case the same property is available in several units @@ -38,6 +53,12 @@ ebas_matrix = ["aerosol", "pm10", "pm25"] [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 -"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_sulfate_aerosol_in_air" +# 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" +#"" = "" +#"" = "" diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 25519bc..fba4030 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -13,11 +13,15 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): engine = "actrisebas" station_filter = { - "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + "stations": { + "include": ["Birkenes II", "Jungfraujoch", "Ispra", "Melpitz", "Westerland"] + }, } - vars_to_read = ["ozone mass concentration"] - pyaerocom_vars_to_read = ["conco3"] + # vars_to_read = ["ozone mass concentration"] + vars_to_read = ["aerosol particle sulphate 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: @@ -72,11 +76,12 @@ def test_api_reading_small_data_set(self): engine = pyaro.list_timeseries_engines()[self.engine] # with engine.open( - filters=filters, + # filters=[], + filters=self.station_filter, vars_to_read=self.vars_to_read, ) as ts: self.assertGreaterEqual(len(ts.variables()), 1) - self.assertEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts.stations()), 2) self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) @@ -90,17 +95,19 @@ def test_api_reading_pyaerocom_naming(self): # "include": self.vars_to_read, # }, } - engine = pyaro.list_timeseries_engines()[self.engine] - # - with engine.open( - filters=filters, - vars_to_read=self.pyaerocom_vars_to_read, - test_flag=True, - ) as ts: - self.assertGreaterEqual(len(ts.variables()), 1) - self.assertEqual(len(ts.stations()), 2) - self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) - self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) + # 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], + test_flag=False, + ) 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) # # # From c23167618af58d137452c69fc54eabeaf4c9b859 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 23 Sep 2024 16:50:21 +0200 Subject: [PATCH 38/60] WIP: added more variables --- src/pyaro_readers/actrisebas/definitions.toml | 20 +++++++++++++++++++ tests/test_ActrisEbasReader.py | 3 ++- 2 files changed, 22 insertions(+), 1 deletion(-) diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index ea116cf..cc198d9 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -41,6 +41,22 @@ standard_names = ["mass_concentration_of_sulphate_corrected_for_seaspray_express "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] @@ -62,3 +78,7 @@ standard_names = ["mass_concentration_of_sulphate_corrected_for_seaspray_express #"" = "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/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index fba4030..a600392 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -18,7 +18,8 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): }, } # vars_to_read = ["ozone mass concentration"] - vars_to_read = ["aerosol particle sulphate 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"] From d564d7cf1adb36a2b6666c7c0725b7a720956e52 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 1 Oct 2024 16:41:18 +0200 Subject: [PATCH 39/60] WIP --- .../actrisebas/ActrisEbasReader.py | 25 ++++++++++++++++--- src/pyaro_readers/actrisebas/definitions.toml | 3 ++- tests/test_ActrisEbasReader.py | 4 +-- 3 files changed, 25 insertions(+), 7 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 86a26b2..04bd3fe 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -24,8 +24,8 @@ logger = logging.getLogger(__name__) # default API URL base -# BASE_API_URL = "https://prod-actris-md.nilu.no/Vocabulary/categories" 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 @@ -181,9 +181,19 @@ def __init__( retries = Retry(connect=5, read=2, redirect=5) http = PoolManager(retries=retries) response = http.request("GET", query_url) - json_resp_tmp = json.loads(response.data.decode("utf-8")) - json_resp.extend(json_resp_tmp) - page_no += 1 + 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( @@ -401,6 +411,7 @@ def extract_urls( 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: @@ -415,11 +426,17 @@ def extract_urls( 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 diff --git a/src/pyaro_readers/actrisebas/definitions.toml b/src/pyaro_readers/actrisebas/definitions.toml index cc198d9..0731e44 100644 --- a/src/pyaro_readers/actrisebas/definitions.toml +++ b/src/pyaro_readers/actrisebas/definitions.toml @@ -16,7 +16,8 @@ ebas_matrix = ["air"] standard_names = ["mass_concentration_of_ozone_in_air"] [variables.vmro3] -actris_variable = ["ozone amount fraction"] +#actris_variable = ["ozone amount fraction"] +actris_variable = ["ozone mass concentration"] actris_matrix = ["gas phase"] ebas_component = ["ozone"] ebas_matrix = ["air"] diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index a600392..3c1f92b 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -21,8 +21,8 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): # 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"] + pyaerocom_vars_to_read = ["vmro3"] + # pyaerocom_vars_to_read = ["concso4t"] def test_api_online(self, url=TEST_URL): try: From a448c32d37463694d17a981707d4e966896767e4 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 17 Oct 2024 16:37:42 +0200 Subject: [PATCH 40/60] bump version --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 0204dfd..bd45d72 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.10.dev3 +version = 0.0.10.dev4 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md @@ -21,7 +21,7 @@ url = https://github.com/metno/pyaro-readers [options] python_version = >=3.10 install_requires = - pyaro >= 0.0.10 + pyaro >= 0.0.12 geocoder_reverse_natural_earth >= 0.0.2 netCDF4 requests From 511a7498c536f3cc0787a3d6f3bf16872df15a71 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 18 Oct 2024 14:14:28 +0200 Subject: [PATCH 41/60] WIP read data with seperate read() call instead of start reading during init --- .../actrisebas/ActrisEbasReader.py | 219 ++++++++++-------- tests/test_ActrisEbasReader.py | 41 ++-- 2 files changed, 135 insertions(+), 125 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 04bd3fe..ec1cc2b 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -90,7 +90,7 @@ def __init__( self._filename = None self.vars_to_read = vars_to_read self._stations = {} - self._urls_to_dl = {} + self.urls_to_dl = {} self._data = {} # var -> {data-array} self._set_filters(filters) # self._header = [] @@ -99,7 +99,7 @@ def __init__( # 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 = {} + self.standard_names = {} # _laststatstr = "" self._revision = datetime.datetime.now() self._metadata["revision"] = datetime.datetime.strftime( @@ -124,44 +124,44 @@ def __init__( self.sites_to_exclude = [] # 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 + 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 = {} + 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"]: - # use gave a pyaerocom variable name - self._actris_vars_to_read[var] = self._def_data["variables"][var][ + 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]: + for _actris_var in self.actris_vars_to_read[var]: try: - self._standard_names[var].extend( + self.standard_names[var].extend( self.get_actris_standard_name(_actris_var) ) - self._standard_names[_actris_var].extend( + self.standard_names[_actris_var].extend( self.get_actris_standard_name(_actris_var) ) except KeyError: - self._standard_names[var] = self.get_actris_standard_name( + self.standard_names[var] = self.get_actris_standard_name( _actris_var ) - self._standard_names[ + 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) + 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: + 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 _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__)), @@ -176,7 +176,7 @@ def __init__( 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}" + 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) @@ -196,7 +196,7 @@ def __init__( continue self._metadata[_pyaro_var][_actris_var] = json_resp - self._urls_to_dl[_actris_var] = self.extract_urls( + 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, @@ -204,99 +204,112 @@ def __init__( # 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] + # 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_data( + def read( self, - actris_variable: str, - urls_to_dl: dict, tqdm_desc="reading stations", ): """ read the data from EBAS thredds server """ - 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]): - 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: - bla = f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" - logger.info( - f"station {site_name}, file #{f_idx}: found matching standard_name {std_name}" - ) + # 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: + 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), + ) - 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 actris_variable not in self._data: - self._data[actris_variable] = NpStructuredData( - actris_variable, - 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": site_name, + "longitude": lon[0], + "latitude": lat[0], + "altitude": altitude[0], + "country": self.get_ebas_data_country_code(tmp_data), + "url": "", + "long_name": stat_code, + } ) - - self._data[actris_variable].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 - break - if not site_name in self._stations: - self._stations[site_name] = Station( - { - "station": site_name, - "longitude": lon[0], - "latitude": lat[0], - "altitude": altitude[0], - "country": self.get_ebas_data_country_code(tmp_data), - "url": "", - "long_name": stat_code, - } - ) - bar.update(1) - bar.close() + bar.update(1) + bar.close() def get_ebas_flags(self, url: str = EBAS_FLAG_URL) -> dict: """small helper to download the bas flag file from NILU""" @@ -362,7 +375,7 @@ def get_ebas_data_country_code(self, tmp_data): 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] + 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!" @@ -387,7 +400,7 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non # if defined, return only names that match if ( tmp_data[data_var].attrs["units"] - == self._def_data["actris_std_units"][data_var] + == self.def_data["actris_std_units"][data_var] ): data_vars.append(data_var) except KeyError: diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 3c1f92b..29ac0d7 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -75,18 +75,16 @@ def test_api_reading_small_data_set(self): # }, } engine = pyaro.list_timeseries_engines()[self.engine] - # - with engine.open( - # filters=[], - 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.assertIn("revision", ts.metadata()) + read_obj = engine.open( + filters=self.station_filter, vars_to_read=self.vars_to_read + ) + read_obj.read() + self.assertGreaterEqual(len(read_obj.variables()), 1) + self.assertGreaterEqual(len(read_obj.stations()), 2) + self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) + self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) + self.assertGreaterEqual(len(read_obj.variables()), 1) + self.assertIn("revision", read_obj.metadata()) def test_api_reading_pyaerocom_naming(self): # test access to the EBAS API @@ -99,16 +97,15 @@ def test_api_reading_pyaerocom_naming(self): # 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], - test_flag=False, - ) 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) + read_obj = engine.open(filters=self.station_filter, vars_to_read=[_var]) + read_obj.read() + self.assertGreaterEqual(len(read_obj.variables()), 1) + self.assertGreaterEqual(len(read_obj.stations()), 2) + self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) + self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) + self.assertGreaterEqual(len(read_obj.variables()), 1) + self.assertIn("revision", read_obj.metadata()) + # # # From d5198a0c91fe2fd22d04ac2be411bfa8d54f2ee1 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 21 Oct 2024 16:38:54 +0200 Subject: [PATCH 42/60] WIP: intergrate separate reading call --- .../actrisebas/ActrisEbasReader.py | 3 ++ .../AeronetSdaTimeseriesReader.py | 6 ++- .../AeronetSunTimeseriesReader.py | 23 ++++++-- tests/test_AERONETTimeSeriesReader.py | 52 ++++++++++++++----- tests/test_ActrisEbasReader.py | 48 ++++++++++++----- 5 files changed, 99 insertions(+), 33 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index ec1cc2b..fd2d555 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -5,6 +5,7 @@ import tomllib from urllib.parse import urlparse, quote +from contextlib import contextmanager import numpy as np import polars @@ -213,6 +214,7 @@ def __init__( def metadata(self): return self._metadata + @contextmanager def read( self, tqdm_desc="reading stations", @@ -310,6 +312,7 @@ def read( ) bar.update(1) bar.close() + yield self def get_ebas_flags(self, url: str = EBAS_FLAG_URL) -> dict: """small helper to download the bas flag file from NILU""" diff --git a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py index ebd6236..3d57b51 100644 --- a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py @@ -5,6 +5,8 @@ from urllib.parse import urlparse from urllib.request import urlopen from zipfile import BadZipFile, ZipFile +from contextlib import contextmanager + import datetime import numpy as np @@ -101,10 +103,12 @@ 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 # check if file is a URL + _laststatstr = "" if self.is_valid_url(self._filename): # try to open as zipfile try: diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 0d94e5d..feb8ce0 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -3,6 +3,7 @@ from urllib.parse import urlparse from urllib.request import urlopen from zipfile import BadZipFile, ZipFile +from contextlib import contextmanager from geocoder_reverse_natural_earth import ( Geocoder_Reverse_NE, @@ -90,9 +91,19 @@ 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 + + + @contextmanager + def read( + self, + tqdm_desc="reading stations", + ): # check if file is a URL + _laststatstr = "" if self.is_valid_url(self._filename): # try to open as zipfile try: @@ -128,7 +139,7 @@ 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 +184,8 @@ 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: @@ -198,6 +209,7 @@ def __init__( value, station, lat, lon, alt, start, end, Flag.VALID, np.nan ) bar.close() + yield self def metadata(self): return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) @@ -273,5 +285,8 @@ def open(self, filename, *args, **kwargs) -> AeronetSunTimeseriesReader: def description(self): return "Simple reader of AeronetSun-files using the pyaro infrastructure" + def read(self): + return self.reader_class().read(*args, **kwargs) + def url(self): return "https://github.com/metno/pyaro-readers" diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index 5f8ef09..ea4b302 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -33,12 +33,13 @@ 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( + read_obj = engine.open( TEST_URL, filters=[], fill_country_flag=False, tqdm_desc="test_dl_data_unzipped", - ) as ts: + ) + with read_obj.read() as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -46,16 +47,34 @@ 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}") engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - with engine.open( + read_obj = engine.open( TEST_ZIP_URL, filters=[], fill_country_flag=False, tqdm_desc="test_dl_data_zipped", - ) as ts: + ) + with read_obj.read() as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -70,12 +89,13 @@ def test_aeronet_data_zipped(self): if not self.external_resource_available(AERONETSUN_URL): self.skipTest(f"external resource not available: {AERONETSUN_URL}") engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - with engine.open( + read_obj = engine.open( AERONETSUN_URL, filters=[], fill_country_flag=False, tqdm_desc="aeronet data zipped", - ) as ts: + ) + with read_obj.read() as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -89,9 +109,10 @@ def test_init(self): # just see that it doesn't fail engine.description() engine.args() - with engine.open( + read_obj = engine.open( self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" - ) as ts: + ) + with read_obj.read() as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -101,9 +122,10 @@ def test_init(self): def test_stationfilter(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) - with engine.open( + read_obj = engine.open( self.file, filters=[sfilter], tqdm_desc="test_stationfilter" - ) as ts: + ) + with read_obj.read() as ts: count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -113,9 +135,10 @@ def test_stationfilter(self): def test_wrappers(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] new_var_name = "od500aer" - with VariableNameChangingReader( + read_obj = VariableNameChangingReader( engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} - ) as ts: + ) + with read_obj.read() as ts: self.assertEqual(ts.data(new_var_name).variable, new_var_name) pass @@ -125,9 +148,10 @@ def test_variables_filter(self): vfilter = pyaro.timeseries.filters.get( "variables", reader_to_new={"AOD_550nm": new_var_name} ) - with engine.open( + read_obj = engine.open( self.file, filters=[vfilter], tqdm_desc="test_variables_filter" - ) as ts: + ) + with read_obj.read() as ts: self.assertEqual(ts.data(new_var_name).variable, new_var_name) diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 29ac0d7..fba50f7 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -78,13 +78,33 @@ def test_api_reading_small_data_set(self): read_obj = engine.open( filters=self.station_filter, vars_to_read=self.vars_to_read ) - read_obj.read() - self.assertGreaterEqual(len(read_obj.variables()), 1) - self.assertGreaterEqual(len(read_obj.stations()), 2) - self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) - self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) - self.assertGreaterEqual(len(read_obj.variables()), 1) - self.assertIn("revision", read_obj.metadata()) + with read_obj.read() as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertGreaterEqual(len(read_obj.stations()), 2) + self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) + self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) + self.assertGreaterEqual(len(read_obj.variables()), 1) + self.assertIn("revision", read_obj.metadata()) + + # def test_api_reading_small_data_set_without_cm(self): + # # test access to the EBAS API + # filters = { + # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + # # "variables": { + # # "include": self.vars_to_read, + # # }, + # } + # engine = pyaro.list_timeseries_engines()[self.engine] + # read_obj = engine.open( + # filters=self.station_filter, vars_to_read=self.vars_to_read + # ) + # read_obj.read() + # self.assertGreaterEqual(len(read_obj.variables()), 1) + # self.assertGreaterEqual(len(read_obj.stations()), 2) + # self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) + # self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) + # self.assertGreaterEqual(len(read_obj.variables()), 1) + # self.assertIn("revision", read_obj.metadata()) def test_api_reading_pyaerocom_naming(self): # test access to the EBAS API @@ -98,13 +118,13 @@ def test_api_reading_pyaerocom_naming(self): for _var in self.pyaerocom_vars_to_read: engine = pyaro.list_timeseries_engines()[self.engine] read_obj = engine.open(filters=self.station_filter, vars_to_read=[_var]) - read_obj.read() - self.assertGreaterEqual(len(read_obj.variables()), 1) - self.assertGreaterEqual(len(read_obj.stations()), 2) - self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) - self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) - self.assertGreaterEqual(len(read_obj.variables()), 1) - self.assertIn("revision", read_obj.metadata()) + with read_obj.read() as ts: + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertGreaterEqual(len(ts.stations()), 2) + self.assertGreaterEqual(len(ts._data[read_obj.variables()[0]]), 1000) + self.assertGreaterEqual(len(ts.data(read_obj.variables()[0])), 1000) + self.assertGreaterEqual(len(ts.variables()), 1) + self.assertIn("revision", ts.metadata()) # From 979cc2786826e84c55aa2df1d451f290ddbebdd4 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 28 Oct 2024 16:15:06 +0100 Subject: [PATCH 43/60] WIP: intergrate separate reading call #2 --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 3 +++ tests/test_ActrisEbasReader.py | 12 +++++++++++- 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index fd2d555..4857b86 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -495,3 +495,6 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return reader_class().reader.read diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index fba50f7..ff545ac 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -139,7 +139,17 @@ def test_api_reading_pyaerocom_naming(self): # self.assertEqual(ts.data(new_var_name).variable, new_var_name) # pass # # - + def test_wrappers(self): + engine = pyaro.list_timeseries_engines()[self.engine] + new_var_name = "vmro3" + ebas_var_name = "ozone mass concentration" + # read_obj = engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]) + blubb = VariableNameChangingReader(engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]), reader_to_new={ebas_var_name: new_var_name}) + # with VariableNameChangingReader. + # with blubb.reader.read() as ts: + with blubb.read() as ts: + self.assertEqual(ts.data(new_var_name).variable, new_var_name) + pass if __name__ == "__main__": unittest.main() From 91f2502f0e625e4e67891f22078e12a0211adea4 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Tue, 29 Oct 2024 13:49:35 +0100 Subject: [PATCH 44/60] WIP: refactoring to use a separate read method implementing a context manager for the actrisebas reader --- .../actrisebas/ActrisEbasReader.py | 4 +- tests/test_ActrisEbasReader.py | 51 +++++-------------- 2 files changed, 17 insertions(+), 38 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 4857b86..2c0f07d 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -496,5 +496,7 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + @contextmanager def read(self): - return reader_class().reader.read + with self.reader_class().read() as ts: + yield ts diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index ff545ac..1880f79 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -26,7 +26,7 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): def test_api_online(self, url=TEST_URL): try: - req = urllib.request.Request(TEST_URL, method="HEAD") + req = urllib.request.Request(url, method="HEAD") resp = urllib.request.urlopen(req) resp.url return True @@ -58,22 +58,14 @@ def test_flag_list_online(self): engine.description() assert engine.args() - # def test_api_reading(self): - # # test access to the EBAS API - # filters={"variables": {"include": ["ozone mass concentration", ]}} - # engine = pyaro.list_timeseries_engines()[self.engine] - # with engine.open(filters=filters) as ts: - # # test that the definitions file could be read properly - # self.assertGreaterEqual(len(ts.variables()), 2) - # def test_api_reading_small_data_set(self): # test access to the EBAS API - filters = { - "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - # "variables": { - # "include": self.vars_to_read, - # }, - } + # filters = { + # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, + # # "variables": { + # # "include": self.vars_to_read, + # # }, + # } engine = pyaro.list_timeseries_engines()[self.engine] read_obj = engine.open( filters=self.station_filter, vars_to_read=self.vars_to_read @@ -108,12 +100,6 @@ def test_api_reading_small_data_set(self): def test_api_reading_pyaerocom_naming(self): # test access to the EBAS API - filters = { - "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - # "variables": { - # "include": self.vars_to_read, - # }, - } # test variable by variable for _var in self.pyaerocom_vars_to_read: engine = pyaro.list_timeseries_engines()[self.engine] @@ -127,28 +113,19 @@ def test_api_reading_pyaerocom_naming(self): self.assertIn("revision", ts.metadata()) - # - # # - # def test_wrappers(self): - # engine = pyaro.list_timeseries_engines()[self.engine] - # new_var_name = "vmro3" - # with VariableNameChangingReader( - # engine.open(vars_to_read=self.vars_to_read, filters=self.station_filter), - # {self.vars_to_read[0]: new_var_name} - # ) as ts: - # self.assertEqual(ts.data(new_var_name).variable, new_var_name) - # pass - # # def test_wrappers(self): engine = pyaro.list_timeseries_engines()[self.engine] new_var_name = "vmro3" ebas_var_name = "ozone mass concentration" # read_obj = engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]) - blubb = VariableNameChangingReader(engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]), reader_to_new={ebas_var_name: new_var_name}) - # with VariableNameChangingReader. - # with blubb.reader.read() as ts: - with blubb.read() as ts: + read_obj = VariableNameChangingReader(engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]), + reader_to_new={ebas_var_name: new_var_name}) + with read_obj.read() 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(read_obj.variables()[0])), 1000) + self.assertIn("revision", ts.metadata()) pass if __name__ == "__main__": From 6a8b53ba2b05b5d4f892dcc9e89105a32a036f43 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Wed, 30 Oct 2024 16:05:58 +0100 Subject: [PATCH 45/60] adjust 1st readers to new read method --- .../actrisebas/ActrisEbasReader.py | 52 ++++++------- .../AeronetSdaTimeseriesReader.py | 15 ++-- .../AeronetSunTimeseriesReader.py | 35 ++++----- tests/test_AERONETSDATimeSeriesReader.py | 8 ++ tests/test_AERONETTimeSeriesReader.py | 42 +++++------ tests/test_ActrisEbasReader.py | 75 +++++-------------- 6 files changed, 97 insertions(+), 130 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 2c0f07d..bfd69bb 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -3,9 +3,7 @@ import logging import os import tomllib - from urllib.parse import urlparse, quote -from contextlib import contextmanager import numpy as np import polars @@ -80,12 +78,12 @@ class ActrisEbasTestDataNotFoundException(Exception): 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, + vars_to_read: list[str] = None, + filters=[], + tqdm_desc: str | None = None, + ts_type: str = "daily", + test_flag: bool = False, ): """ """ self._filename = None @@ -214,10 +212,9 @@ def __init__( def metadata(self): return self._metadata - @contextmanager def read( - self, - tqdm_desc="reading stations", + self, + tqdm_desc="reading stations", ): """ read the data from EBAS thredds server @@ -226,7 +223,7 @@ def read( # for pyaerocom vocabulary they are not (key is pyaerocom variable name there)! for _var in self.actris_vars_to_read: for actris_variable in self.actris_vars_to_read[_var]: - # actris_variable = self.actris_vars_to_read[_var][0] + # 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) @@ -237,9 +234,9 @@ def read( # 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, - ) + 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) @@ -312,7 +309,6 @@ def read( ) bar.update(1) bar.close() - yield self def get_ebas_flags(self, url: str = EBAS_FLAG_URL) -> dict: """small helper to download the bas flag file from NILU""" @@ -323,7 +319,7 @@ def get_ebas_flags(self, url: str = EBAS_FLAG_URL) -> dict: for var in df.columns: ret_data[var] = df[var].to_numpy() - # for simplicity add a dict entry listing the valis flags + # 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"] @@ -402,8 +398,8 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non try: # if defined, return only names that match if ( - tmp_data[data_var].attrs["units"] - == self.def_data["actris_std_units"][data_var] + tmp_data[data_var].attrs["units"] + == self.def_data["actris_std_units"][data_var] ): data_vars.append(data_var) except KeyError: @@ -412,10 +408,10 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non return data_vars def extract_urls( - self, - json_resp: dict, - sites_to_read: list[str] = [], - sites_to_exclude: list[str] = [], + 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 @@ -436,11 +432,11 @@ def extract_urls( # 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] + site_data[DISTRIBUTION_ROOT_KEY] ): if ( - distribution_data[DISTRIBUTION_PROTOCOL_KEY] - != DISTRIBUTION_PROTOCOL_NAME + distribution_data[DISTRIBUTION_PROTOCOL_KEY] + != DISTRIBUTION_PROTOCOL_NAME ): logger.info( f"skipping site: {site_name} / proto: {distribution_data[DISTRIBUTION_PROTOCOL_KEY]}" @@ -496,7 +492,5 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - @contextmanager def read(self): - with self.reader_class().read() as ts: - yield ts + return self.reader_class().read() diff --git a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py index 3d57b51..59cf9ed 100644 --- a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py @@ -5,7 +5,6 @@ from urllib.parse import urlparse from urllib.request import urlopen from zipfile import BadZipFile, ZipFile -from contextlib import contextmanager import datetime @@ -106,7 +105,9 @@ def __init__( 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 = "" if self.is_valid_url(self._filename): @@ -175,7 +176,7 @@ def __init__( gcd = Geocoder_Reverse_NE() crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) - bar = tqdm(desc=tqdm_desc, total=len(lines)) + bar = tqdm(desc=self.tqdm_desc, total=len(lines)) for _ridx, row in enumerate(crd): bar.update(1) if row[SITE_NAME] != _laststatstr: @@ -185,7 +186,7 @@ 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 +231,8 @@ 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: @@ -332,3 +333,7 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() + diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index feb8ce0..e20b7bc 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -1,16 +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 -from contextlib import contextmanager +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, @@ -18,8 +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" @@ -60,12 +60,12 @@ class AeronetSunTimeseriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( - self, - filename, - filters=[], - fill_country_flag: bool = FILL_COUNTRY_FLAG, - tqdm_desc: str | None = None, - ts_type: str = "daily", + self, + filename, + filters=[], + fill_country_flag: bool = FILL_COUNTRY_FLAG, + tqdm_desc: str | None = None, + ts_type: str = "daily", ): """open a new Aeronet timeseries-reader @@ -96,8 +96,6 @@ def __init__( self.fill_country_flag = fill_country_flag self.ts_type = ts_type - - @contextmanager def read( self, tqdm_desc="reading stations", @@ -209,7 +207,6 @@ def read( value, station, lat, lon, alt, start, end, Flag.VALID, np.nan ) bar.close() - yield self def metadata(self): return dict(revision=datetime.datetime.strftime(self._revision, "%y%m%d%H%M%S")) @@ -227,7 +224,7 @@ def close(self): pass def compute_od_from_angstromexp( - self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float + self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float ) -> float: """Compute AOD at specified wavelength @@ -254,7 +251,7 @@ def compute_od_from_angstromexp( return od_ref * (lambda_ref / to_lambda) ** angstrom_coeff def calc_angstroem_coeff( - self, od1: float, od2: float, wl1: float, wl2: float + self, od1: float, od2: float, wl1: float, wl2: float ) -> float: """ small helper method to calculate angstroem coefficient @@ -285,8 +282,8 @@ def open(self, filename, *args, **kwargs) -> AeronetSunTimeseriesReader: def description(self): return "Simple reader of AeronetSun-files using the pyaro infrastructure" - def read(self): - return self.reader_class().read(*args, **kwargs) - def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() diff --git a/tests/test_AERONETSDATimeSeriesReader.py b/tests/test_AERONETSDATimeSeriesReader.py index 62ad014..30e9da4 100644 --- a/tests/test_AERONETSDATimeSeriesReader.py +++ b/tests/test_AERONETSDATimeSeriesReader.py @@ -42,6 +42,7 @@ def test_dl_data_tared(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_tared", ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -60,6 +61,7 @@ def test_dl_data_unzipped(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_unzipped", ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -78,6 +80,7 @@ def test_dl_data_zipped(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_zipped", ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -100,6 +103,7 @@ def test_aeronet_data_zipped(self): fill_country_flag=False, tqdm_desc="aeronet SDA data zipped", ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -118,6 +122,7 @@ def test_init(self): with engine.open( self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -130,6 +135,7 @@ def test_stationfilter(self): with engine.open( self.file, filters=[sfilter], tqdm_desc="test_stationfilter" ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -143,6 +149,7 @@ def test_wrappers(self): engine.open(self.file, filters=[]), {"Coarse_Mode_AOD_500nm[tau_c]": new_var_name}, ) as ts: + ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) pass @@ -155,6 +162,7 @@ def test_variables_filter(self): with engine.open( self.file, filters=[vfilter], tqdm_desc="test_sda_variables_filter" ) as ts: + ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index ea4b302..f6c4706 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -33,13 +33,13 @@ 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"] - read_obj = engine.open( + with engine.open( TEST_URL, filters=[], fill_country_flag=False, tqdm_desc="test_dl_data_unzipped", - ) - with read_obj.read() as ts: + ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -68,13 +68,13 @@ 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}") engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - read_obj = engine.open( + with engine.open( TEST_ZIP_URL, filters=[], fill_country_flag=False, tqdm_desc="test_dl_data_zipped", - ) - with read_obj.read() as ts: + ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -89,13 +89,13 @@ def test_aeronet_data_zipped(self): if not self.external_resource_available(AERONETSUN_URL): self.skipTest(f"external resource not available: {AERONETSUN_URL}") engine = pyaro.list_timeseries_engines()["aeronetsunreader"] - read_obj = engine.open( + with engine.open( AERONETSUN_URL, filters=[], fill_country_flag=False, tqdm_desc="aeronet data zipped", - ) - with read_obj.read() as ts: + ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -109,10 +109,10 @@ def test_init(self): # just see that it doesn't fail engine.description() engine.args() - read_obj = engine.open( + with engine.open( self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" - ) - with read_obj.read() as ts: + ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -122,10 +122,10 @@ def test_init(self): def test_stationfilter(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] sfilter = pyaro.timeseries.filters.get("stations", exclude=["Cuiaba"]) - read_obj = engine.open( + with engine.open( self.file, filters=[sfilter], tqdm_desc="test_stationfilter" - ) - with read_obj.read() as ts: + ) as ts: + ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -135,10 +135,10 @@ def test_stationfilter(self): def test_wrappers(self): engine = pyaro.list_timeseries_engines()["aeronetsunreader"] new_var_name = "od500aer" - read_obj = VariableNameChangingReader( + with VariableNameChangingReader( engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} - ) - with read_obj.read() as ts: + ) as ts: + ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) pass @@ -148,10 +148,10 @@ def test_variables_filter(self): vfilter = pyaro.timeseries.filters.get( "variables", reader_to_new={"AOD_550nm": new_var_name} ) - read_obj = engine.open( + with engine.open( self.file, filters=[vfilter], tqdm_desc="test_variables_filter" - ) - with read_obj.read() as ts: + ) 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 index 1880f79..4ee3760 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -22,6 +22,7 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): 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): @@ -33,16 +34,6 @@ def test_api_online(self, url=TEST_URL): except: return False - # def test_vocabulary(self, url=TEST_URL): - # try: - # req = urllib.request.Request(TEST_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") @@ -59,74 +50,46 @@ def test_flag_list_online(self): assert engine.args() def test_api_reading_small_data_set(self): - # test access to the EBAS API - # filters = { - # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - # # "variables": { - # # "include": self.vars_to_read, - # # }, - # } engine = pyaro.list_timeseries_engines()[self.engine] - read_obj = engine.open( - filters=self.station_filter, vars_to_read=self.vars_to_read - ) - with read_obj.read() as ts: + with engine.open( + filters=self.station_filter, vars_to_read=self.vars_to_read + ) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) - self.assertGreaterEqual(len(read_obj.stations()), 2) - self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) - self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) - self.assertGreaterEqual(len(read_obj.variables()), 1) - self.assertIn("revision", read_obj.metadata()) - - # def test_api_reading_small_data_set_without_cm(self): - # # test access to the EBAS API - # filters = { - # "stations": {"include": ["Birkenes II", "Jungfraujoch"]}, - # # "variables": { - # # "include": self.vars_to_read, - # # }, - # } - # engine = pyaro.list_timeseries_engines()[self.engine] - # read_obj = engine.open( - # filters=self.station_filter, vars_to_read=self.vars_to_read - # ) - # read_obj.read() - # self.assertGreaterEqual(len(read_obj.variables()), 1) - # self.assertGreaterEqual(len(read_obj.stations()), 2) - # self.assertGreaterEqual(len(read_obj._data[read_obj.variables()[0]]), 1000) - # self.assertGreaterEqual(len(read_obj.data(read_obj.variables()[0])), 1000) - # self.assertGreaterEqual(len(read_obj.variables()), 1) - # self.assertIn("revision", read_obj.metadata()) + 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] - read_obj = engine.open(filters=self.station_filter, vars_to_read=[_var]) - with read_obj.read() as ts: + with engine.open(filters=self.station_filter, vars_to_read=[_var]) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) self.assertGreaterEqual(len(ts.stations()), 2) - self.assertGreaterEqual(len(ts._data[read_obj.variables()[0]]), 1000) - self.assertGreaterEqual(len(ts.data(read_obj.variables()[0])), 1000) + 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_wrappers(self): engine = pyaro.list_timeseries_engines()[self.engine] new_var_name = "vmro3" ebas_var_name = "ozone mass concentration" - # read_obj = engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]) - read_obj = VariableNameChangingReader(engine.open(filters=self.station_filter, vars_to_read=[ebas_var_name]), - reader_to_new={ebas_var_name: new_var_name}) - with read_obj.read() as ts: + 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: + ts.read() 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(read_obj.variables()[0])), 1000) + self.assertGreaterEqual(len(ts.data(ts.variables()[0])), 1000) self.assertIn("revision", ts.metadata()) pass + if __name__ == "__main__": unittest.main() From f54f9d02ea3d29b379493ce7fbc483223b0c8709 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Wed, 30 Oct 2024 16:29:57 +0100 Subject: [PATCH 46/60] WIP: adjust readers to new read method --- .../ascii2netcdf/Ascii2NetcdfTimeseries.py | 10 +++++++++- tests/test_Ascii2NetcdfTimeseries.py | 3 +++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py index 1c4d1af..d4dd994 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( @@ -283,3 +287,7 @@ 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/tests/test_Ascii2NetcdfTimeseries.py b/tests/test_Ascii2NetcdfTimeseries.py index 403ee43..f9b0caa 100644 --- a/tests/test_Ascii2NetcdfTimeseries.py +++ b/tests/test_Ascii2NetcdfTimeseries.py @@ -20,6 +20,7 @@ def test_1open(self): with pyaro.open_timeseries( self.engine, EBAS_URL, resolution="daily", filters=[] ) as ts: + ts.read() self.assertGreater(len(ts.variables()), 70) self.assertGreater(len(ts.stations()), 300) @@ -29,6 +30,7 @@ def test_2read(self): with pyaro.open_timeseries( self.engine, EBAS_URL, resolution="daily", filters=[] ) as ts: + ts.read() data = ts.data("sulphur_dioxide_in_air") self.assertIn("AM0001", data.stations) self.assertGreater(np.sum(data.values), 10000) @@ -45,6 +47,7 @@ def test_3read(self): "stations": {"include": ["NO0002"]}, }, # Birkenes2 ) as ts: + ts.read() data = ts.data("sulphur_dioxide_in_air") self.assertIn("NO0002", data.stations) self.assertGreater(len(data), 360) From 59c4f7f2e4e9aa6e625456d4a82d4755a0b1450a Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 31 Oct 2024 13:39:09 +0100 Subject: [PATCH 47/60] WIP: adjust harpreader tp separate read() method --- setup.cfg | 2 +- src/pyaro_readers/harpreader/harpreader.py | 8 +++++++- tests/test_HARPReader.py | 4 +++- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/setup.cfg b/setup.cfg index bd45d72..190da85 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = pyaro_readers -version = 0.0.10.dev4 +version = 0.0.10.dev5 author = MET Norway description = implementations of pyaerocom reading plugings using pyaro as interface long_description = file: README.md diff --git a/src/pyaro_readers/harpreader/harpreader.py b/src/pyaro_readers/harpreader/harpreader.py index 4116667..78ee631 100644 --- a/src/pyaro_readers/harpreader/harpreader.py +++ b/src/pyaro_readers/harpreader/harpreader.py @@ -73,6 +73,9 @@ def __init__( else: self._files.append(file) + def read(self): + """reading method""" + bar = tqdm(total=len(self._files)) for f_idx, _file in enumerate(self._files): @@ -84,7 +87,7 @@ 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: @@ -238,3 +241,6 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() diff --git a/tests/test_HARPReader.py b/tests/test_HARPReader.py index 2820d62..d70decc 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"] @@ -26,6 +26,7 @@ def test_1read(self): self.file, vars_to_read=self.test_vars, ) as ts: + ts.read() for _v_idx, var in enumerate(self.test_vars): data = ts.data(var) self.assertGreater(len(data), 10000) @@ -44,6 +45,7 @@ def test_2open_directory(self): with pyaro.open_timeseries( self.engine, self.testdata_dir, filters=[], vars_to_read=self.test_vars ) as ts: + ts.read() for _v_idx, var in enumerate(self.test_vars): data = ts.data(var) assert isinstance(data.units, str) From 5f243e6633e345d7e65189001f711e5ed56ffc81 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 31 Oct 2024 14:05:22 +0100 Subject: [PATCH 48/60] WIP: make all readers imporatble with separate read() method --- .../eeareader/EEATimeseriesReader.py | 21 ++++++++++----- .../netcdf_rw/Netcdf_RWTimeseries.py | 8 ++++++ .../NILUPMFAbsorptionReader.py | 25 ++++++++++++------ .../nilupmfebas/EbasPmfReader.py | 26 +++++++++++++------ tests/test_EEAReader.py | 1 + tests/test_EbasPmfTimeSeriesReader.py | 2 ++ tests/test_NILUPMFAbsorptionReader.py | 2 ++ 7 files changed, 63 insertions(+), 22 deletions(-) diff --git a/src/pyaro_readers/eeareader/EEATimeseriesReader.py b/src/pyaro_readers/eeareader/EEATimeseriesReader.py index cdabd3a..1fee85e 100644 --- a/src/pyaro_readers/eeareader/EEATimeseriesReader.py +++ b/src/pyaro_readers/eeareader/EEATimeseriesReader.py @@ -72,9 +72,15 @@ def __init__( self._data = {} # var -> {data-array} self._set_filters(filters) - self.metadata = self._read_metadata(filename) + self._metadata = self._read_metadata(filename) + self._filters = filters - self._read_polars(filters, filename) + def read(self): + """reading method quick and dirty""" + self._read_polars(self._filters, self._filename) + + def metadata(self) -> dict[str, str]: + return self._metadata def _read_polars(self, filters, filename) -> None: try: @@ -163,7 +169,7 @@ def _read_polars(self, filters, filename) -> None: continue df = lf - station_metadata = self.metadata[df.row(0)[0].split("/")[-1]] + station_metadata = self._metadata[df.row(0)[0].split("/")[-1]] file_unit = df.row(0)[df.get_column_index("Unit")] @@ -223,7 +229,7 @@ def _filter_dates( ) def _read_metadata(self, folder: str) -> dict: - metadata = {} + _metadata = {} filename = Path(folder) / "metadata.csv" if not filename.exists(): raise FileExistsError(f"Metadata file could not be found in {folder}") @@ -237,7 +243,7 @@ def _read_metadata(self, folder: str) -> dict: alt = float(words[5]) except: continue - metadata[words[0]] = { + _metadata[words[0]] = { "lon": lon, "lat": lat, "alt": alt, @@ -245,7 +251,7 @@ def _read_metadata(self, folder: str) -> dict: "country": words[1], } - return metadata + return _metadata def _unfiltered_data(self, varname) -> Data: return self._data[varname] @@ -272,3 +278,6 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() diff --git a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py index 09696f3..99961ac 100644 --- a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py +++ b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py @@ -55,6 +55,9 @@ def __init__( else: os.path.makedirs(filename) + def read(self): + """standard read method""" + dataglob = os.path.join(self._directory, f"{self.ncfile_prefix}.????.nc") self._years = set() for file in glob.iglob(dataglob): @@ -76,6 +79,7 @@ def iterate_files(self): if os.path.exists(file_path): yield file_path + def metadata(self): metadata = dict() date = datetime.datetime.min @@ -371,3 +375,7 @@ 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 d19737d..44e91ea 100644 --- a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py +++ b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py @@ -73,25 +73,31 @@ def __init__( self._set_filters(filters) self._header = [] self._revision = datetime.datetime.min + self._filename = filename + self._fill_country_flag = fill_country_flag + self._file_mask = file_mask + self._tqdm_desc = tqdm_desc - if Path(filename).is_file(): - self._filename = filename - self._process_file(self._filename, fill_country_flag) + def read(self): + """ read method""" - elif Path(filename).is_dir(): - files_pathlib = Path(filename).glob(file_mask) + 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)) + 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: @@ -231,3 +237,6 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + + def read(self): + return self.reader_class().read() \ No newline at end of file diff --git a/src/pyaro_readers/nilupmfebas/EbasPmfReader.py b/src/pyaro_readers/nilupmfebas/EbasPmfReader.py index 0cbb0fe..065659f 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 +59,29 @@ 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""" + + if Path(self._realpath).is_dir(): # search directory for files - files = list(realpath.glob(filemask)) - bar = tqdm(desc=tqdm_desc, total=len(files)) + 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() @@ -266,6 +273,9 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" + def read(self): + return self.reader_class().read() + class ReadEbasOptions(dict): """Options for EBAS reading routine diff --git a/tests/test_EEAReader.py b/tests/test_EEAReader.py index 44aad7d..cb4aa31 100644 --- a/tests/test_EEAReader.py +++ b/tests/test_EEAReader.py @@ -30,6 +30,7 @@ def test_1open_files(self): self.testdata_dir, filters={"variables": {"include": ["PM10", "SO2"]}}, ) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 2) self.assertGreaterEqual(len(ts.stations()), 2) for var in ts.variables(): diff --git a/tests/test_EbasPmfTimeSeriesReader.py b/tests/test_EbasPmfTimeSeriesReader.py index e015fce..d642999 100644 --- a/tests/test_EbasPmfTimeSeriesReader.py +++ b/tests/test_EbasPmfTimeSeriesReader.py @@ -54,6 +54,7 @@ def test_0engine(self): def test_1open_single_file(self): with pyaro.open_timeseries(self.engine, self.file, filters=[]) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars @@ -63,6 +64,7 @@ def test_1open_single_file(self): def test_2open_directory(self): with pyaro.open_timeseries(self.engine, self.testdata_dir, filters=[]) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars diff --git a/tests/test_NILUPMFAbsorptionReader.py b/tests/test_NILUPMFAbsorptionReader.py index 94a267b..607b516 100644 --- a/tests/test_NILUPMFAbsorptionReader.py +++ b/tests/test_NILUPMFAbsorptionReader.py @@ -26,6 +26,7 @@ def test_0engine(self): def test_1open_single_file(self): with pyaro.open_timeseries(self.engine, self.file, filters=[]) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars @@ -36,6 +37,7 @@ def test_1open_single_file(self): def test_2open_directory(self): with pyaro.open_timeseries(self.engine, self.testdata_dir, filters=[]) as ts: + ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars From bb331090d1f32897afd993bb5c01515695899d21 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 31 Oct 2024 14:05:49 +0100 Subject: [PATCH 49/60] bump needed pyaro version --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 190da85..35686b9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -21,7 +21,7 @@ url = https://github.com/metno/pyaro-readers [options] python_version = >=3.10 install_requires = - pyaro >= 0.0.12 + pyaro >= 0.0.14 geocoder_reverse_natural_earth >= 0.0.2 netCDF4 requests From cbbdbcfd798e4912a20c4b7b059a84138d0f11eb Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 7 Nov 2024 11:24:54 +0100 Subject: [PATCH 50/60] read data on access only --- src/pyaro_readers/actrisebas/ActrisEbasReader.py | 8 ++++++-- tests/test_ActrisEbasReader.py | 4 ---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index bfd69bb..d4efd2c 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -222,6 +222,9 @@ def read( # 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] @@ -453,12 +456,15 @@ def extract_urls( 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): @@ -492,5 +498,3 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - def read(self): - return self.reader_class().read() diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 4ee3760..7e27c8a 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -54,7 +54,6 @@ def test_api_reading_small_data_set(self): with engine.open( filters=self.station_filter, vars_to_read=self.vars_to_read ) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 1) self.assertGreaterEqual(len(ts.stations()), 2) self.assertGreaterEqual(len(ts._data[ts.variables()[0]]), 1000) @@ -68,12 +67,10 @@ def test_api_reading_pyaerocom_naming(self): 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: - ts.read() 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_wrappers(self): @@ -82,7 +79,6 @@ def test_wrappers(self): 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: - ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) self.assertGreaterEqual(len(ts.variables()), 1) self.assertGreaterEqual(len(ts.stations()), 2) From a3819018a408a5792462e93235e6167f10c3da58 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 7 Nov 2024 14:03:56 +0100 Subject: [PATCH 51/60] read data on access only --- .../AeronetSdaTimeseriesReader.py | 15 +++++++++------ .../AeronetSunTimeseriesReader.py | 11 ++++++++--- tests/test_AERONETSDATimeSeriesReader.py | 8 -------- tests/test_AERONETTimeSeriesReader.py | 6 ------ 4 files changed, 17 insertions(+), 23 deletions(-) diff --git a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py index 59cf9ed..53001fe 100644 --- a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py @@ -110,6 +110,9 @@ def __init__( 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: @@ -134,7 +137,7 @@ def read(self): lines = [] _fidx = 0 members = tf.getmembers() - bar = tqdm(desc="extracting tar file...", total=len(members)) + bar = tqdm(desc="extracting tar file...", total=len(members), disable=None) for _midx, member in enumerate(members): if fnmatch(member.name, FILE_MASK): bar.update(1) @@ -176,7 +179,7 @@ def read(self): gcd = Geocoder_Reverse_NE() crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) - bar = tqdm(desc=self.tqdm_desc, total=len(lines)) + 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: @@ -272,15 +275,19 @@ def read(self): 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): @@ -333,7 +340,3 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - - def read(self): - return self.reader_class().read() - diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index e20b7bc..3e19dd2 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -102,6 +102,9 @@ def read( ): # 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: @@ -127,7 +130,7 @@ def read( gcd = Geocoder_Reverse_NE() crd = csv.DictReader(lines, fieldnames=self._fields, delimiter=DELIMITER) - bar = tqdm(desc=tqdm_desc, total=len(lines)) + bar = tqdm(desc=tqdm_desc, total=len(lines), disable=None) for _ridx, row in enumerate(crd): bar.update(1) if row[SITE_NAME] != _laststatstr: @@ -209,15 +212,19 @@ def read( 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): @@ -285,5 +292,3 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - def read(self): - return self.reader_class().read() diff --git a/tests/test_AERONETSDATimeSeriesReader.py b/tests/test_AERONETSDATimeSeriesReader.py index 30e9da4..62ad014 100644 --- a/tests/test_AERONETSDATimeSeriesReader.py +++ b/tests/test_AERONETSDATimeSeriesReader.py @@ -42,7 +42,6 @@ def test_dl_data_tared(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_tared", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -61,7 +60,6 @@ def test_dl_data_unzipped(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_unzipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -80,7 +78,6 @@ def test_dl_data_zipped(self): fill_country_flag=False, tqdm_desc="test_sda_dl_data_zipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -103,7 +100,6 @@ def test_aeronet_data_zipped(self): fill_country_flag=False, tqdm_desc="aeronet SDA data zipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -122,7 +118,6 @@ def test_init(self): with engine.open( self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -135,7 +130,6 @@ def test_stationfilter(self): with engine.open( self.file, filters=[sfilter], tqdm_desc="test_stationfilter" ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -149,7 +143,6 @@ def test_wrappers(self): engine.open(self.file, filters=[]), {"Coarse_Mode_AOD_500nm[tau_c]": new_var_name}, ) as ts: - ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) pass @@ -162,7 +155,6 @@ def test_variables_filter(self): with engine.open( self.file, filters=[vfilter], tqdm_desc="test_sda_variables_filter" ) as ts: - ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) diff --git a/tests/test_AERONETTimeSeriesReader.py b/tests/test_AERONETTimeSeriesReader.py index f6c4706..3b50d0b 100644 --- a/tests/test_AERONETTimeSeriesReader.py +++ b/tests/test_AERONETTimeSeriesReader.py @@ -39,7 +39,6 @@ def test_dl_data_unzipped(self): fill_country_flag=False, tqdm_desc="test_dl_data_unzipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -74,7 +73,6 @@ def test_dl_data_zipped(self): fill_country_flag=False, tqdm_desc="test_dl_data_zipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -95,7 +93,6 @@ def test_aeronet_data_zipped(self): fill_country_flag=False, tqdm_desc="aeronet data zipped", ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -112,7 +109,6 @@ def test_init(self): with engine.open( self.file, filters=[], fill_country_flag=True, tqdm_desc="test_init" ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -125,7 +121,6 @@ def test_stationfilter(self): with engine.open( self.file, filters=[sfilter], tqdm_desc="test_stationfilter" ) as ts: - ts.read() count = 0 for var in ts.variables(): count += len(ts.data(var)) @@ -138,7 +133,6 @@ def test_wrappers(self): with VariableNameChangingReader( engine.open(self.file, filters=[]), {"AOD_500nm": new_var_name} ) as ts: - ts.read() self.assertEqual(ts.data(new_var_name).variable, new_var_name) pass From 5c86d2baaded2608e238096ff8e1103234bd8327 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 7 Nov 2024 15:13:45 +0100 Subject: [PATCH 52/60] read data on access only --- src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py | 6 +----- src/pyaro_readers/harpreader/harpreader.py | 9 +++++++-- src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py | 5 ++--- .../nilupmfabsorptionreader/NILUPMFAbsorptionReader.py | 7 ++++++- src/pyaro_readers/nilupmfebas/EbasPmfReader.py | 6 ++++++ tests/test_Ascii2NetcdfTimeseries.py | 3 --- tests/test_EbasPmfTimeSeriesReader.py | 2 -- tests/test_HARPReader.py | 2 -- tests/test_NILUPMFAbsorptionReader.py | 2 -- 9 files changed, 22 insertions(+), 20 deletions(-) diff --git a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py index d4dd994..3fa36da 100644 --- a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py +++ b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py @@ -73,7 +73,7 @@ def __init__( self._metadata = self.metadata() - def read(self): + # def read(self): self._variables = self._read_file_variables() station_file = "StationList.csv" station_filepath = os.path.join(self._directory, station_file) @@ -287,7 +287,3 @@ 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/harpreader/harpreader.py b/src/pyaro_readers/harpreader/harpreader.py index 2c97c71..cde6696 100644 --- a/src/pyaro_readers/harpreader/harpreader.py +++ b/src/pyaro_readers/harpreader/harpreader.py @@ -75,7 +75,9 @@ def __init__( 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): @@ -217,12 +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 99961ac..2d35be0 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: @@ -55,9 +57,6 @@ def __init__( else: os.path.makedirs(filename) - def read(self): - """standard read method""" - dataglob = os.path.join(self._directory, f"{self.ncfile_prefix}.????.nc") self._years = set() for file in glob.iglob(dataglob): diff --git a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py index 0105cfb..d0d9c8f 100644 --- a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py +++ b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py @@ -80,7 +80,9 @@ def __init__( 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) @@ -200,12 +202,15 @@ 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 a04c20a..51dcca9 100644 --- a/src/pyaro_readers/nilupmfebas/EbasPmfReader.py +++ b/src/pyaro_readers/nilupmfebas/EbasPmfReader.py @@ -64,6 +64,9 @@ def __init__( 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(self._realpath.glob(self._filemask)) @@ -221,12 +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_Ascii2NetcdfTimeseries.py b/tests/test_Ascii2NetcdfTimeseries.py index f9b0caa..403ee43 100644 --- a/tests/test_Ascii2NetcdfTimeseries.py +++ b/tests/test_Ascii2NetcdfTimeseries.py @@ -20,7 +20,6 @@ def test_1open(self): with pyaro.open_timeseries( self.engine, EBAS_URL, resolution="daily", filters=[] ) as ts: - ts.read() self.assertGreater(len(ts.variables()), 70) self.assertGreater(len(ts.stations()), 300) @@ -30,7 +29,6 @@ def test_2read(self): with pyaro.open_timeseries( self.engine, EBAS_URL, resolution="daily", filters=[] ) as ts: - ts.read() data = ts.data("sulphur_dioxide_in_air") self.assertIn("AM0001", data.stations) self.assertGreater(np.sum(data.values), 10000) @@ -47,7 +45,6 @@ def test_3read(self): "stations": {"include": ["NO0002"]}, }, # Birkenes2 ) as ts: - ts.read() data = ts.data("sulphur_dioxide_in_air") self.assertIn("NO0002", data.stations) self.assertGreater(len(data), 360) diff --git a/tests/test_EbasPmfTimeSeriesReader.py b/tests/test_EbasPmfTimeSeriesReader.py index d642999..e015fce 100644 --- a/tests/test_EbasPmfTimeSeriesReader.py +++ b/tests/test_EbasPmfTimeSeriesReader.py @@ -54,7 +54,6 @@ def test_0engine(self): def test_1open_single_file(self): with pyaro.open_timeseries(self.engine, self.file, filters=[]) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars @@ -64,7 +63,6 @@ def test_1open_single_file(self): def test_2open_directory(self): with pyaro.open_timeseries(self.engine, self.testdata_dir, filters=[]) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars diff --git a/tests/test_HARPReader.py b/tests/test_HARPReader.py index d70decc..856de84 100644 --- a/tests/test_HARPReader.py +++ b/tests/test_HARPReader.py @@ -26,7 +26,6 @@ def test_1read(self): self.file, vars_to_read=self.test_vars, ) as ts: - ts.read() for _v_idx, var in enumerate(self.test_vars): data = ts.data(var) self.assertGreater(len(data), 10000) @@ -45,7 +44,6 @@ def test_2open_directory(self): with pyaro.open_timeseries( self.engine, self.testdata_dir, filters=[], vars_to_read=self.test_vars ) as ts: - ts.read() for _v_idx, var in enumerate(self.test_vars): data = ts.data(var) assert isinstance(data.units, str) diff --git a/tests/test_NILUPMFAbsorptionReader.py b/tests/test_NILUPMFAbsorptionReader.py index 607b516..94a267b 100644 --- a/tests/test_NILUPMFAbsorptionReader.py +++ b/tests/test_NILUPMFAbsorptionReader.py @@ -26,7 +26,6 @@ def test_0engine(self): def test_1open_single_file(self): with pyaro.open_timeseries(self.engine, self.file, filters=[]) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars @@ -37,7 +36,6 @@ def test_1open_single_file(self): def test_2open_directory(self): with pyaro.open_timeseries(self.engine, self.testdata_dir, filters=[]) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 1) for var in ts.variables(): assert var in self.test_vars From b155f31e30cbedec9182d1fe85864e17349dcf22 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Thu, 7 Nov 2024 16:41:54 +0100 Subject: [PATCH 53/60] WIP --- tests/test_PyerocomBinding.py | 79 +++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 tests/test_PyerocomBinding.py diff --git a/tests/test_PyerocomBinding.py b/tests/test_PyerocomBinding.py new file mode 100644 index 0000000..1f2db19 --- /dev/null +++ b/tests/test_PyerocomBinding.py @@ -0,0 +1,79 @@ +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"] + + # Try testing the pyaerocom binding if pyaerocom is installed + try: + from pyaerocom.io import ReadUngridded + pyaerocom_installed_flag = True + except ImportError: + pyaerocom_installed_flag = False + pass + + AERONETVAR = "od440aer" + + + 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_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()) + + + +if __name__ == "__main__": + unittest.main() From 2c7a86cdc28c943101b1d0f96e71dc7f057c177c Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 8 Nov 2024 13:04:20 +0100 Subject: [PATCH 54/60] put the full station name at the right place for pyaerocom --- .../actrisebas/ActrisEbasReader.py | 21 ++++++++++++++++--- 1 file changed, 18 insertions(+), 3 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index d4efd2c..478e7fe 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -87,7 +87,10 @@ def __init__( ): """ """ self._filename = None - self.vars_to_read = vars_to_read + 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} @@ -122,6 +125,16 @@ def __init__( 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 @@ -301,17 +314,19 @@ def read( if not site_name in self._stations: self._stations[site_name] = Station( { - "station": site_name, + "station": stat_code, "longitude": lon[0], "latitude": lat[0], "altitude": altitude[0], "country": self.get_ebas_data_country_code(tmp_data), "url": "", - "long_name": stat_code, + # 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""" From 1465a3a583ae99c692712477414da7d02fdaaa28 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 8 Nov 2024 13:05:09 +0100 Subject: [PATCH 55/60] enable setting the country for a station by default --- .../aeronetsunreader/AeronetSunTimeseriesReader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index 3e19dd2..f61fcd0 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -48,7 +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"), From 5bd7ac55f825abdd570b5bb017cbc89225efbad3 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 8 Nov 2024 13:06:52 +0100 Subject: [PATCH 56/60] add some actrisebas reading tests --- tests/test_PyerocomBinding.py | 98 ++++++++++++++++++++++------------- 1 file changed, 62 insertions(+), 36 deletions(-) diff --git a/tests/test_PyerocomBinding.py b/tests/test_PyerocomBinding.py index 1f2db19..bcbe390 100644 --- a/tests/test_PyerocomBinding.py +++ b/tests/test_PyerocomBinding.py @@ -1,15 +1,7 @@ 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): +class TestPyaroReaderPyaerocom(unittest.TestCase): engine = "actrisebas" station_filter = { @@ -17,23 +9,8 @@ class TestActrisEbasTimeSeriesReader(unittest.TestCase): "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"] - - # Try testing the pyaerocom binding if pyaerocom is installed - try: - from pyaerocom.io import ReadUngridded - pyaerocom_installed_flag = True - except ImportError: - pyaerocom_installed_flag = False - pass - AERONETVAR = "od440aer" + ACTRISEBASVAR = "concso4t" def test_pyaerocom_aeronet(self): @@ -60,18 +37,67 @@ def test_pyaerocom_aeronet(self): 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) + + 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.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) - 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()) From 434d2f9ab597e805eab2f1b0138e3015f96c7c23 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Mon, 11 Nov 2024 15:18:00 +0100 Subject: [PATCH 57/60] add some more pyaerocom testing --- tests/test_PyerocomBinding.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/tests/test_PyerocomBinding.py b/tests/test_PyerocomBinding.py index bcbe390..aa327ab 100644 --- a/tests/test_PyerocomBinding.py +++ b/tests/test_PyerocomBinding.py @@ -11,6 +11,7 @@ class TestPyaroReaderPyaerocom(unittest.TestCase): } AERONETVAR = "od440aer" ACTRISEBASVAR = "concso4t" + ACTRISEBASVARLIST = ["concso4t","concso4c"] def test_pyaerocom_aeronet(self): @@ -65,6 +66,7 @@ def test_pyaerocom_actrisebas_single_var(self): 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 @@ -86,7 +88,7 @@ def test_pyaerocom_actrisebas_many_var(self): } # 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.ACTRISEBASVAR + url = self.ACTRISEBASVARLIST obsconfig = PyaroConfig( name=data_name, data_id=data_id, @@ -97,6 +99,9 @@ def test_pyaerocom_actrisebas_many_var(self): 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) From 19ed717a19246985d21791e66bdf389bde86d2c6 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 20 Dec 2024 11:04:05 +0100 Subject: [PATCH 58/60] go back to Python 3.10 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index d61abd9..14c9c27 100644 --- a/setup.cfg +++ b/setup.cfg @@ -64,7 +64,7 @@ min_version = 4.0 skip_missing_interpreters = True isolated_build = True env_list = - py311 + py310 format #depends = From 89df726724b571d7d89ea436b6de407d6eaea1ab Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 20 Dec 2024 11:04:29 +0100 Subject: [PATCH 59/60] linting --- .../actrisebas/ActrisEbasReader.py | 45 ++++++++++--------- .../AeronetSdaTimeseriesReader.py | 6 ++- .../AeronetSunTimeseriesReader.py | 21 +++++---- .../ascii2netcdf/Ascii2NetcdfTimeseries.py | 2 +- .../netcdf_rw/Netcdf_RWTimeseries.py | 2 - .../NILUPMFAbsorptionReader.py | 6 ++- tests/test_ActrisEbasReader.py | 8 ++-- tests/test_PyerocomBinding.py | 29 +++++++----- 8 files changed, 67 insertions(+), 52 deletions(-) diff --git a/src/pyaro_readers/actrisebas/ActrisEbasReader.py b/src/pyaro_readers/actrisebas/ActrisEbasReader.py index 478e7fe..6875085 100644 --- a/src/pyaro_readers/actrisebas/ActrisEbasReader.py +++ b/src/pyaro_readers/actrisebas/ActrisEbasReader.py @@ -78,12 +78,12 @@ class ActrisEbasTestDataNotFoundException(Exception): 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, + vars_to_read: list[str] = None, + filters=[], + tqdm_desc: str | None = None, + ts_type: str = "daily", + test_flag: bool = False, ): """ """ self._filename = None @@ -226,8 +226,8 @@ def metadata(self): return self._metadata def read( - self, - tqdm_desc="reading stations", + self, + tqdm_desc="reading stations", ): """ read the data from EBAS thredds server @@ -250,12 +250,14 @@ def read( # 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, - ) + 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) + 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" @@ -416,8 +418,8 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non try: # if defined, return only names that match if ( - tmp_data[data_var].attrs["units"] - == self.def_data["actris_std_units"][data_var] + tmp_data[data_var].attrs["units"] + == self.def_data["actris_std_units"][data_var] ): data_vars.append(data_var) except KeyError: @@ -426,10 +428,10 @@ def _get_ebas_data_vars(self, tmp_data, actris_var: str = None, units: str = Non return data_vars def extract_urls( - self, - json_resp: dict, - sites_to_read: list[str] = [], - sites_to_exclude: list[str] = [], + 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 @@ -450,11 +452,11 @@ def extract_urls( # 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] + site_data[DISTRIBUTION_ROOT_KEY] ): if ( - distribution_data[DISTRIBUTION_PROTOCOL_KEY] - != DISTRIBUTION_PROTOCOL_NAME + distribution_data[DISTRIBUTION_PROTOCOL_KEY] + != DISTRIBUTION_PROTOCOL_NAME ): logger.info( f"skipping site: {site_name} / proto: {distribution_data[DISTRIBUTION_PROTOCOL_KEY]}" @@ -512,4 +514,3 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - diff --git a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py index 53001fe..425cf3d 100644 --- a/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsdareader/AeronetSdaTimeseriesReader.py @@ -137,7 +137,11 @@ def read(self): lines = [] _fidx = 0 members = tf.getmembers() - bar = tqdm(desc="extracting tar file...", total=len(members), disable=None) + bar = tqdm( + desc="extracting tar file...", + total=len(members), + disable=None, + ) for _midx, member in enumerate(members): if fnmatch(member.name, FILE_MASK): bar.update(1) diff --git a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py index f61fcd0..b7a8525 100644 --- a/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py +++ b/src/pyaro_readers/aeronetsunreader/AeronetSunTimeseriesReader.py @@ -60,12 +60,12 @@ class AeronetSunTimeseriesReader(AutoFilterReaderEngine.AutoFilterReader): def __init__( - self, - filename, - filters=[], - fill_country_flag: bool = FILL_COUNTRY_FLAG, - tqdm_desc: str | None = None, - ts_type: str = "daily", + self, + filename, + filters=[], + fill_country_flag: bool = FILL_COUNTRY_FLAG, + tqdm_desc: str | None = None, + ts_type: str = "daily", ): """open a new Aeronet timeseries-reader @@ -97,8 +97,8 @@ def __init__( self.ts_type = ts_type def read( - self, - tqdm_desc="reading stations", + self, + tqdm_desc="reading stations", ): # check if file is a URL _laststatstr = "" @@ -231,7 +231,7 @@ def close(self): pass def compute_od_from_angstromexp( - self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float + self, to_lambda: float, od_ref: float, lambda_ref: float, angstrom_coeff: float ) -> float: """Compute AOD at specified wavelength @@ -258,7 +258,7 @@ def compute_od_from_angstromexp( return od_ref * (lambda_ref / to_lambda) ** angstrom_coeff def calc_angstroem_coeff( - self, od1: float, od2: float, wl1: float, wl2: float + self, od1: float, od2: float, wl1: float, wl2: float ) -> float: """ small helper method to calculate angstroem coefficient @@ -291,4 +291,3 @@ def description(self): def url(self): return "https://github.com/metno/pyaro-readers" - diff --git a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py index 3fa36da..59a749c 100644 --- a/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py +++ b/src/pyaro_readers/ascii2netcdf/Ascii2NetcdfTimeseries.py @@ -73,7 +73,7 @@ def __init__( self._metadata = self.metadata() - # def read(self): + # def read(self): self._variables = self._read_file_variables() station_file = "StationList.csv" station_filepath = os.path.join(self._directory, station_file) diff --git a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py index 2d35be0..942f213 100644 --- a/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py +++ b/src/pyaro_readers/netcdf_rw/Netcdf_RWTimeseries.py @@ -78,7 +78,6 @@ def iterate_files(self): if os.path.exists(file_path): yield file_path - def metadata(self): metadata = dict() date = datetime.datetime.min @@ -377,4 +376,3 @@ def url(self): 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 d0d9c8f..2a6a3c6 100644 --- a/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py +++ b/src/pyaro_readers/nilupmfabsorptionreader/NILUPMFAbsorptionReader.py @@ -79,7 +79,7 @@ def __init__( self._tqdm_desc = tqdm_desc def read(self): - """ read method""" + """read method""" # check if the data has been read already if len(self._data) != 0: return @@ -99,7 +99,9 @@ def read(self): bar.update(1) self._process_file(file, self._fill_country_flag) else: - raise ValueError(f"Given filename {self._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: diff --git a/tests/test_ActrisEbasReader.py b/tests/test_ActrisEbasReader.py index 7e27c8a..a62092a 100644 --- a/tests/test_ActrisEbasReader.py +++ b/tests/test_ActrisEbasReader.py @@ -52,7 +52,7 @@ def test_flag_list_online(self): 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 + 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) @@ -77,8 +77,10 @@ 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: + 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) diff --git a/tests/test_PyerocomBinding.py b/tests/test_PyerocomBinding.py index aa327ab..0e84254 100644 --- a/tests/test_PyerocomBinding.py +++ b/tests/test_PyerocomBinding.py @@ -11,8 +11,7 @@ class TestPyaroReaderPyaerocom(unittest.TestCase): } AERONETVAR = "od440aer" ACTRISEBASVAR = "concso4t" - ACTRISEBASVARLIST = ["concso4t","concso4c"] - + ACTRISEBASVARLIST = ["concso4t", "concso4c"] def test_pyaerocom_aeronet(self): # test reading via pyaerocom @@ -20,7 +19,7 @@ def test_pyaerocom_aeronet(self): from pyaerocom.io.pyaro.pyaro_config import PyaroConfig from pyaerocom.io import ReadUngridded except ImportError: - assert("pyaerocom not installed") + assert "pyaerocom not installed" return data_name = "aeronettest" @@ -44,14 +43,20 @@ def test_pyaerocom_actrisebas_single_var(self): from pyaerocom.io.pyaro.pyaro_config import PyaroConfig from pyaerocom.io import ReadUngridded except ImportError: - assert("pyaerocom not installed") + assert "pyaerocom not installed" return data_name = "PYARO_actrisebas" data_id = "actrisebas" station_filter = { "stations": { - "include": ["Birkenes II", "Jungfraujoch", "Ispra", "Melpitz", "Westerland"] + "include": [ + "Birkenes II", + "Jungfraujoch", + "Ispra", + "Melpitz", + "Westerland", + ] }, } # needs to be the variable name for actrisebas @@ -75,16 +80,22 @@ def test_pyaerocom_actrisebas_many_var(self): from pyaerocom.io.pyaro.pyaro_config import PyaroConfig from pyaerocom.io import ReadUngridded except ImportError: - assert("pyaerocom not installed") + assert "pyaerocom not installed" return data_name = "PYARO_actrisebas" data_id = "actrisebas" station_filter = { "stations": { - "include": ["Birkenes II", "Jungfraujoch", "Ispra", "Melpitz", "Westerland"] + "include": [ + "Birkenes II", + "Jungfraujoch", + "Ispra", + "Melpitz", + "Westerland", + ] }, - "variables": {"include": ["concso4t", "concso4c"]} + "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) @@ -104,7 +115,5 @@ def test_pyaerocom_actrisebas_many_var(self): self.assertIn(url[1], data.contains_vars) - - if __name__ == "__main__": unittest.main() From c362cfb7cb0f86a61d2deeb5252086d8745d3315 Mon Sep 17 00:00:00 2001 From: Jan Griesfeller Date: Fri, 20 Dec 2024 14:59:59 +0100 Subject: [PATCH 60/60] go back to main-dev's version --- tests/test_EEAReader.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_EEAReader.py b/tests/test_EEAReader.py index 4c2d25c..7e04f91 100644 --- a/tests/test_EEAReader.py +++ b/tests/test_EEAReader.py @@ -32,7 +32,6 @@ def test_1open_files(self): self.engine, self.testdata_dir, ) as ts: - ts.read() self.assertGreaterEqual(len(ts.variables()), 2) self.assertGreaterEqual(len(ts.stations()), 2) self.assertTrue(set(self.test_vars).issubset(ts.variables()))