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Commit f80a434d authored by Carsten Hinz's avatar Carsten Hinz
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added a auxillary class to provide the same loggers to all examples and scripts 

Adopted two notebooks to use the new logging
used conversionOfTimestamps script for testing of auxillary class.
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2 merge requests!11Creation of first beta release version,!8Resolve "add structured logging and output levels for complete module"
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examples/produce_data_manyStations.ipynb
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%% Cell type:code id: tags:
``` python
import logging
from datetime import datetime as dt
from collections import namedtuple
from pathlib import Path
from toargridding.toar_rest_client import AnalysisServiceDownload, Connection
from toargridding.grids import RegularGrid
from toargridding.gridding import get_gridded_toar_data
from toargridding.metadata import TimeSample
from toargridding.defaultLogging import toargridding_defaultLogging
logger = toargridding_defaultLogging()
logger.addShellLogger(logging.DEBUG)
```
%% Cell type:code id: tags:
``` python
#creation of request.
Config = namedtuple("Config", ["grid", "time", "variables", "stats", "moreOptions"])
grid = RegularGrid( lat_resolution=1.9, lon_resolution=2.5, )
configs = dict()
for year in range (0,19):
valid_data = Config(
grid,
TimeSample( start=dt(2000+year,1,1), end=dt(2000+year,12,31), sampling="daily"),#possibly adopt range:-)
["mole_fraction_of_ozone_in_air"],#variable name
[ "dma8epa_strict" ]# change to dma8epa_strict
)
configs[f"test_ta{year}"] = valid_data
```
%% Cell type:code id: tags:
``` python
#CAVE: the request takes over 30min per requested year. Therefore this cell needs to be executed at different times to check, if the results are ready for download.
#the processing is done on the server of the TOAR database.
#a restart of the cell continues the request to the REST API if the requested data are ready for download
# The download can also take a few minutes
stats_endpoint = "https://toar-data.fz-juelich.de/api/v2/analysis/statistics/"
cache_basepath = Path("cache")
result_basepath = Path("results")
cache_basepath.mkdir(exist_ok=True)
result_basepath.mkdir(exist_ok=True)
analysis_service = AnalysisServiceDownload(stats_endpoint=stats_endpoint, cache_dir=cache_basepath, sample_dir=result_basepath, use_downloaded=True)
#here we adopt the durations before, a request is stopped.
#the default value is 30 minutes.
#waiting up to 3h for one request
analysis_service.connection.setRequestTimes(interval_min=45, maxWait_min=12*60)
for person, config in configs.items():
print(f"\nProcessing {person}:")
print(f"--------------------")
datasets, metadatas = get_gridded_toar_data(
analysis_service=analysis_service,
grid=config.grid,
time=config.time,
variables=config.variables,
stats=config.stats,
)
for dataset, metadata in zip(datasets, metadatas):
dataset.to_netcdf(result_basepath / f"{metadata.get_id()}_{config.grid.get_id()}.nc")
print(metadata.get_id())
```
......
examples/produce_data_withOptional.ipynb
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%% Cell type:code id: tags:
``` python
import logging
from datetime import datetime as dt
from collections import namedtuple
from pathlib import Path
from toargridding.toar_rest_client import AnalysisServiceDownload, Connection
from toargridding.grids import RegularGrid
from toargridding.gridding import get_gridded_toar_data
from toargridding.metadata import TimeSample
from toargridding.defaultLogging import toargridding_defaultLogging
logger = toargridding_defaultLogging()
logger.addShellLogger(logging.DEBUG)
```
%% Cell type:code id: tags:
``` python
#creation of request.
Config = namedtuple("Config", ["grid", "time", "variables", "stats","moreOptions"])
#moreOptions is implemented as a dict to add additional arguments to the query to the REST API
#For example the field toar1_category with its possible values Urban, RuralLowElevation, RuralHighElevation and Unclassified can be added.
#see page 18 in https://toar-data.fz-juelich.de/sphinx/TOAR_UG_Vol03_Database/build/latex/toardatabase--userguide.pdf
#or type_of_area with urban, suburban and rural on page 20 can be used
details4Query ={
#"toar1_category" : "Urban" #uncomment if wished:-)
#"toar1_category" : "RuralLowElevation" #uncomment if wished:-)
#"toar1_category" : "RuralHighElevation" #uncomment if wished:-)
#"type_of_area" : "Urban" #also test Rural, Suburban,
"type_of_area" : "Rural" #also test Rural, Suburban,
#"type_of_area" : "Suburban" #also test Rural, Suburban,
}
grid = RegularGrid( lat_resolution=1.9, lon_resolution=2.5, )
configs = dict()
for year in range(0,19):
valid_data = Config(
grid,
TimeSample( start=dt(2000+year,1,1), end=dt(2000+year,12,31), sampling="daily"),#possibly adopt range:-)
["mole_fraction_of_ozone_in_air"],#variable name
#[ "mean", "dma8epax"],# will start one request after another other...
[ "dma8epa_strict" ],
details4Query
)
configs[f"test_ta{year}"] = valid_data
```
%% Cell type:code id: tags:
``` python
#CAVE: this cell runs about 45minutes per requested year. therefore we increase the waiting duration to 1h per request.
#the processing is done on the server of the TOAR database.
#a restart of the cell continues the request to the REST API if the requested data are ready for download
# The download can also take a few minutes
stats_endpoint = "https://toar-data.fz-juelich.de/api/v2/analysis/statistics/"
cache_basepath = Path("cache")
result_basepath = Path("results")
cache_basepath.mkdir(exist_ok=True)
result_basepath.mkdir(exist_ok=True)
analysis_service = AnalysisServiceDownload(stats_endpoint=stats_endpoint, cache_dir=cache_basepath, sample_dir=result_basepath, use_downloaded=True)
# maybe adopt the interval for requesting the results and the total duration, before the client pauses the requests.
# as the requests take about 45min, it is more suitable to wait 60min before timing out the requests than the original 30min.
analysis_service.connection.setRequestTimes(interval_min=5, maxWait_min=60)
for person, config in configs.items():
print(f"\nProcessing {person}:")
print(f"--------------------")
datasets, metadatas = get_gridded_toar_data(
analysis_service=analysis_service,
grid=config.grid,
time=config.time,
variables=config.variables,
stats=config.stats,
**config.moreOptions
)
for dataset, metadata in zip(datasets, metadatas):
dataset.to_netcdf(result_basepath / f"{metadata.get_id()}_{config.grid.get_id()}.nc")
print(metadata.get_id())
```
......
tests/conversionOfTimestamps.py
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import logging
from logging.handlers import SysLogHandler
from datetime import datetime as dt
from collections import namedtuple
......@@ -8,6 +10,14 @@ from toargridding.grids import RegularGrid
from toargridding.gridding import get_gridded_toar_data
from toargridding.metadata import TimeSample
##setting up logger
from toargridding.defaultLogging import toargridding_defaultLogging
logger = toargridding_defaultLogging()
logger.addShellLogger(logging.DEBUG)
## add logger to syslog
#creation of request.
Config = namedtuple("Config", ["grid", "time", "variables", "stats","moreOptions"])
......
toargridding/defaultLogging.py 0 → 100644
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import logging
from logging.handlers import SysLogHandler
class toargridding_defaultLogging:
"""! class to setup default loggers for toargridding
Methods:
-------
addShellLogger:
adds a formatting logging to the shell. Default level is DEBUG
addSysLogger:
adds a formatted logging to the system log (on a linux system). Default level is WARNING
"""
def __init__(self):
self.logger = logging.getLogger("toargridding")
self.logger.setLevel(logging.DEBUG)
def addShellLogger(self, level=logging.INFO):
"""!adds a formatted logging to the shell to the "toargridding" logger.
The output handler can afterwards be accessed as shell_handler and its formatter as shell_formatter
Parameters:
----------
level:
set the verbosity level of the logger (default: info)
"""
self.shell_handler = logging.StreamHandler()
self.shell_handler.setLevel(level)
self.shell_formatter = logging.Formatter(fmt="%(asctime)s [%(levelname)s] - %(filename)s:%(lineno)d: '%(message)s'", datefmt="%Y-%m-%d %H:%M:%S")
self.shell_handler.setFormatter(self.shell_formatter)
self.logger.addHandler(self.shell_handler)
def addSysLogger(self, level=logging.WARNING):
"""!adds a formatted logging to the system log of a linux system to the "toargridding" logger.
The output handler can afterwards be accessed as syslog_handler and its formatter as syslog_formatter
Parameters:
----------
level:
set the verbosity level of the logger (default: warning)
"""
self.syslog_handler = SysLogHandler(facility=SysLogHandler.LOG_DAEMON, address='/dev/log')
self.syslog_formatter = logging.Formatter(fmt="TOARGRIDDING [%(levelname)s] - %(filename)s:%(lineno)d: '%(message)s'")
self.syslog_handler.setFormatter(self.syslog_formatter)
self.syslog_handler.setLevel(level)
self.logger.addHandler(self.syslog_handler)
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