def test_sos_20_bom_gov_au():
# Setup
service = SensorObservationService(SERVICE_URL, version='2.0.0')
id = service.identification
# Check basic service metadata
assert id.service == 'SOS'
assert id.title == 'KISTERS KiWIS SOS2'
assert id.keywords == []
assert service.provider.name == 'Provider Name'
assert service.provider.contact.name == 'Name'
assert service.provider.contact.position is None
assert len(service.operations) == 5
assert service.get_operation_by_name('GetObservation').methods[0]['url'] == \
'http://bom.gov.au/waterdata/services?datasource=0'
response = service.get_observation(
featureOfInterest='http://bom.gov.au/waterdata/services/stations/181.1',
offerings=['http://bom.gov.au/waterdata/services/tstypes/Pat4_PC_1'],
observedProperties=['http://bom.gov.au/waterdata/services/parameters/Water Course Discharge'],
eventTime='om:phenomenonTime,2016-01-01T00:00:00+10/2016-03-05T00:00:00+10')
# Process WaterML Response
from owslib.etree import etree
from owslib.swe.observation.sos200 import SOSGetObservationResponse
from owslib.swe.observation.waterml2 import MeasurementTimeseriesObservation
et = etree.fromstring(response)
parsed_response = SOSGetObservationResponse(et)
assert len(parsed_response.observations) > 0
for o in parsed_response.observations:
assert isinstance(o, MeasurementTimeseriesObservation)
def sos_observation_xml(url, version='1.0.0', xml=None, offerings=[],
responseFormat=None, observedProperties=[],
eventTime=None, feature=None, allProperties=False):
"""Return the XML from a SOS GetObservation request.
Parameters
----------
url : string
Full HTTP address of SOS
version: string
Version number of the SOS (e.g. 1.0.0)
offerings : list
selected offerings from SOS; defaults to all available
responseFormat : string
desire format for result data
observedProperties : list
filters results for selected properties from SOS; defaults to first one
(unless allProperties is True)
eventTime : string
filters results for a specified instant or period.
Use ISO format YYYY-MM-DDTHH:mm:ss+-HH Periods of time (start and end)
are separated by "/"; e.g. 2009-06-26T10:00:00+01/2009-06-26T11:00:00+01
feature : string
filters results for the ID of a feature_of_interest
allProperties : boolean
if allProperties is True, filters results for all properties (and
ignores any items in the observedProperties)
"""
# GetCapabilites of SOS
_sos = SensorObservationService(url, version=version or '1.0.0', xml=xml or None)
# process any supplied offerings
if offerings:
for off in _sos.offerings: # look for matching IDs
_offerings = [off for off in _sos.offerings if off.id in offerings]
else:
_offerings = []
# get offering IDs to be used
offerings_objs = _offerings or _sos.offerings
sos_offerings = [off.id for off in offerings_objs]
responseFormat = responseFormat or offerings_objs[0].response_formats[0]
if not allProperties:
observedProperties = observedProperties or [offering.observed_properties[0]]
else:
observedProperties = offering.observed_properties
eventTime = eventTime
if feature:
return _sos.get_observation(
offerings=sos_offerings, responseFormat=responseFormat,
observedProperties=observedProperties, eventTime=eventTime,
FEATUREOFINTEREST=feature)
else:
return _sos.get_observation(
offerings=sos_offerings, responseFormat=responseFormat,
observedProperties=observedProperties, eventTime=eventTime)
class IoosSweSos(Collector):
def __init__(self, url, xml=None):
super(IoosSweSos,self).__init__()
self.server = Sos(url, xml=xml)
def metadata(self, **kwargs):
callback = kwargs.get("feature_name_callback", None) or str
kwargs['outputFormat'] = 'text/xml;subtype="sensorML/1.0.1"'
responses = []
if self.features is not None:
for feature in self.features:
kwargs['procedure'] = callback(feature)
responses.append(SensorML(self.server.describe_sensor(**kwargs)))
return responses
def setup_params(self, **kwargs):
params = kwargs
# TODO: BBOX needs to be implemented as an OGC Filter.
# This page has a good example: http://opendap.co-ops.nos.noaa.gov/ioos-dif-sos/index.jsp
# Click on "Collection" in the POST example to see what it should look like.
# Requires changing from GET to POST...
if self.bbox is not None:
print "BBOX requests for IOOS SWE SOS services are not yet implemented"
if self.start_time is not None:
params["eventTime"] = self.start_time.strftime('%Y-%m-%dT%H:%M:%SZ')
if self.end_time is not None:
params["eventTime"] += "/%s" % self.end_time.strftime('%Y-%m-%dT%H:%M:%SZ')
if self.variables is None or len(self.variables) < 1:
raise ValueError("You must set a filter for at least one variable (observedProperty)")
else:
ops = ",".join(self.variables)
if isinstance(ops, basestring):
ops = [ops]
params["observedProperties"] = ops
return params
def collect(self, **kwargs):
kwargs["responseFormat"] = 'text/xml;subtype="om/1.0.0/profiles/ioos_sos/1.0"'
return IoosGetObservation(self.raw(**kwargs)).feature
def raw(self, **kwargs):
params = self.setup_params(**kwargs)
return self.server.get_observation(**params)
def harvest(self):
self.sos = SensorObservationService(self.service.get('url'))
for offering in self.sos.offerings:
# TODO: We assume an offering should only have one procedure here
# which will be the case in sos 2.0, but may not be the case right now
# on some non IOOS supported servers.
uid = offering.procedures[0]
sp_uid = uid.split(":")
# List storing the stations that have already been processed in this SOS server.
# This is kept and checked later to avoid servers that have the same stations in many offerings.
processed = []
# temnplate: urn:ioos:type:authority:id
# sample: ioos:station:wmo:21414
if sp_uid[2] == "station": # Station Offering
if not uid in processed:
self.process_station(uid)
processed.append(uid)
elif sp_uid[2] == "network": # Network Offering
network_ds = IoosDescribeSensor(self.sos.describe_sensor(outputFormat='text/xml;subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"', procedure=uid))
# Iterate over stations in the network and process them individually
for proc in network_ds.procedures:
if proc is not None and proc.split(":")[2] == "station":
if not proc in processed:
self.process_station(proc)
processed.append(proc)
def process_doc(self, doc):
"""
Attempt to parse an xml string conforming to either an SOS or SensorML
dataset and return the results
"""
xml_doc = ET.fromstring(doc)
if xml_doc.tag == "{http://www.opengis.net/sos/1.0}Capabilities":
ds = SensorObservationService(None, xml=doc)
# SensorObservationService does not store the etree doc root,
# so maybe use monkey patching here for now?
ds._root = xml_doc
elif xml_doc.tag == "{http://www.opengis.net/sensorML/1.0.1}SensorML":
ds = SensorML(xml_doc)
else:
raise ValueError("Unrecognized XML root element: {}".format(xml_doc.tag))
return ds
def __init__(self, **kwargs):
super(NdbcSos,self).__init__()
if kwargs.get('test') is True:
url = 'http://sdftest.ndbc.noaa.gov/sos/server.php'
else:
url = 'http://sdf.ndbc.noaa.gov/sos/server.php'
self.server = Sos(url)
class CoopsSos(Collector):
def __init__(self, **kwargs):
super(CoopsSos,self).__init__()
url = 'http://opendap.co-ops.nos.noaa.gov/ioos-dif-sos/SOS'
self.server = Sos(url)
def get_metadata(self, **kwargs):
response = self.server.describe_sensor(**kwargs)
return IoosDescribeSensor(response)
def get_describe_sensor_output_formats(self):
return self.server.get_operation_by_name('DescribeSensor').parameters['outputFormat']['values']
#def get_data(self, **kwargs):
# response = self.get_raw_data(**kwargs)
# return IoosDif(response)
def get_raw_data(self, **kwargs):
res = self.server.get_observation(**kwargs)
if res[41:56] == "ExceptionReport":
res = -1
return res
class NdbcSos(Collector):
def __init__(self, **kwargs):
super(NdbcSos,self).__init__()
if kwargs.get('test') is True:
url = 'http://sdftest.ndbc.noaa.gov/sos/server.php'
else:
url = 'http://sdf.ndbc.noaa.gov/sos/server.php'
self.server = Sos(url)
def get_metadata(self, **kwargs):
response = self.server.describe_sensor(**kwargs)
return IoosDescribeSensor(response)
def get_describe_sensor_output_formats(self):
return self.server.get_operation_by_name('DescribeSensor').parameters['outputFormat']['values']
def get_data(self, **kwargs):
response = self.get_raw_data(**kwargs)
return IoosSwe(response)
def get_raw_data(self, **kwargs):
return self.server.get_observation(**kwargs)
def __init__(self, **kwargs):
super(CoopsSos,self).__init__()
url = 'http://opendap.co-ops.nos.noaa.gov/ioos-dif-sos/SOS'
self.server = Sos(url)
# Accessing ncSOS with OWSLib # <codecell> from owslib.sos import SensorObservationService import pdb from owslib.etree import etree import pandas as pd import datetime as dt # <codecell> # ncSOS endpoint with time series data #url='http://geoport-dev.whoi.edu/thredds/sos/usgs/data2/notebook/1211-A1H.cdf' url='http://www.neracoos.org:8180/thredds/sos/UMO/DSG/SOS/A01/Accelerometer/HistoricRealtime/Agg.ncml' sos = SensorObservationService(url) contents = sos.contents # <codecell> sos.contents # <codecell> off = sos.offerings[1] off.name # <codecell> off.response_formats
import datetime as dt import numpy as np # In[46]: url = 'http://sdf.ndbc.noaa.gov/sos/server.php?request=GetCapabilities&service=SOS&version=1.0.0' ndbc = SensorObservationService(url) # In[47]: # usgs woods hole # buoy data (single current meter) url='http://geoport-dev.whoi.edu/thredds/sos/usgs/data2/notebook/1211-AA.cdf' usgs = SensorObservationService(url) contents = usgs.contents # In[48]: usgs.contents # In[49]: off = usgs.offerings[1] off.name # In[50]:
# <codecell> from owslib.sos import SensorObservationService from owslib.etree import etree import pandas as pd import datetime as dt import matplotlib.pyplot as plt import numpy as np %matplotlib inline # <codecell> # usgs woods hole # regular time series data url='http://geoport-dev.whoi.edu/thredds/sos/usgs/data2/emontgomery/stellwagen/CF-1.6/BUZZ_BAY/2651-A.cdf' usgs = SensorObservationService(url) contents = usgs.contents # <codecell> usgs.contents # <codecell> off = usgs.offerings[1] off.name # <codecell> off.response_formats
def __init__(self, url, xml=None):
super(IoosSweSos, self).__init__()
self.server = Sos(url, xml=xml)
class IoosSweSos(Collector):
def __init__(self, url, xml=None):
super(IoosSweSos, self).__init__()
self.server = Sos(url, xml=xml)
def metadata(self,
output_format=None,
feature_name_callback=None,
**kwargs):
"""
Gets SensorML objects for all procedures in your filtered features.
You should override the default output_format for servers that do not
respond properly.
"""
callback = feature_name_callback or str
if output_format is None:
output_format = (
'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"')
responses = []
if self.features is not None:
for feature in self.features:
ds_kwargs = kwargs.copy()
ds_kwargs.update({
"outputFormat": output_format,
"procedure": callback(feature),
})
responses.append(
SensorML(self.server.describe_sensor(**ds_kwargs)))
return responses
def metadata_plus_exceptions(self,
output_format=None,
feature_name_callback=None,
**kwargs):
"""
Gets SensorML objects for all procedures in your filtered features.
Return two dictionaries for service responses keyed by 'feature':
responses: values are SOS DescribeSensor response text
response_failures: values are exception text content furnished from ServiceException, ExceptionReport
You should override the default output_format for servers that do not
respond properly.
"""
callback = feature_name_callback or str
if output_format is None:
output_format = (
'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"')
responses = {}
response_failures = {}
if self.features is not None:
for feature in self.features:
ds_kwargs = kwargs.copy()
ds_kwargs.update({
"outputFormat": output_format,
"procedure": callback(feature),
})
try:
responses[feature] = SensorML(
self.server.describe_sensor(**ds_kwargs))
except (ServiceException, ExceptionReport) as e:
response_failures[feature] = str(e)
return (responses, response_failures)
def setup_params(self, **kwargs):
params = kwargs
if self.bbox is not None:
params["featureOfInterest"] = "BBOX:%s,%s,%s,%s" % (
self.bbox[0],
self.bbox[1],
self.bbox[2],
self.bbox[3],
)
if self.start_time is not None:
params["eventTime"] = self.start_time.strftime(
"%Y-%m-%dT%H:%M:%SZ")
if self.end_time is not None:
params["eventTime"] += "/%s" % self.end_time.strftime(
"%Y-%m-%dT%H:%M:%SZ")
if self.variables is None or len(self.variables) < 1:
raise ValueError(
"You must set a filter for at least one variable (observedProperty)"
)
else:
ops = ",".join(self.variables)
if isinstance(ops, string_types):
ops = [ops]
params["observedProperties"] = ops
return params
def collect(self, **kwargs):
# there is an unfortunate difference in how 52N and ncSOS handle the response format.
# 52N expects subtype, ncSOS expects schema.
# consult the observed properties and getcaps to figure out which should be used if none passed
if "responseFormat" not in kwargs:
# iterate offerings and see if we need to change to subtype
off_dict = {off.name: off for off in self.server.offerings}
response_format = None
for offering in kwargs.get("offerings", []):
if offering not in off_dict:
continue
ioos_formats = [
rf for rf in off_dict[offering].response_formats
if "ioos_sos/1.0" in rf
]
if not len(ioos_formats):
raise Exception(
"No ioos_sos/1.0 response format found for offering {}"
.format(offering))
if response_format != ioos_formats[0]:
response_format = ioos_formats[0]
kwargs["responseFormat"] = response_format
return IoosGetObservation(self.raw(**kwargs)).observations
def raw(self, **kwargs):
params = self.setup_params(**kwargs)
return self.server.get_observation(**params)
def get_stations_df(self, sos_url, station_urns_sel=None):
""" Returns a Pandas Dataframe
"""
# oFrmts: IOOS SOS OutputFormat strings (first is compliant to the IOOS SOS spec,
# second is to accommodate NDBC). More info here:
# http://ioos.github.io/sos-guidelines/doc/wsdd/sos_wsdd_github_notoc/#describesensor-request:638e0b263020c13a76a55332bd966dbe
oFrmts = [
'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"',
'text/xml;subtype="sensorML/1.0.1"'
]
params = {
'service': 'SOS',
'request': 'GetCapabilities',
'acceptVersions': '1.0.0'
}
sos_url_params = sos_url + '?' + urlencode(params)
# sos_url_params_quoted = quote(sos_url_params,"/=:")
# sos_url_params_unquoted = unquote(sos_url_params)
try:
sosgc = SensorObservationService(sos_url_params)
except (ConnectionError, ReadTimeout) as e:
self.log.write(
u"\nError: unable to connect to SOS service: {url} due to HTTP connection error."
.format(url=sos_url_params))
self.log.write(
u"\nHTTP connection error: {err}.".format(err=str(e)))
sys.exit(
"\nError: unable to connect to SOS service: {url}. \nUnderlying HTTP connection error: {err}"
.format(url=sos_url_params, err=str(e)))
# vars to store returns from sos_collector.metadata_plus_exceptions function:
sml_recs = {}
sml_errors = {}
describe_sensor_url = {}
# leverage Pyoos Collector to query for all available stations and obtain SensorML
# (if station subset not passed in --stations param)
if station_urns_sel is not None:
station_urns = station_urns_sel
else:
sos_collector = IoosSweSos(sos_url)
station_urns = [
urn.name for urn in sos_collector.server.offerings
if 'network' not in urn.name.split(':')
]
sos_collector.features = station_urns
# write out stations in SOS that will be handled:
if self.verbose:
self.log.write(u"\nStations to process for SOS: {sos}".format(
sos=sos_url_params))
print("Stations to process for SOS: {sos}".format(
sos=sos_url_params))
for feature in sos_collector.features:
self.log.write(u"\n - {feature}".format(feature=feature))
print(" - {feature}".format(feature=feature))
# iterate over possible oFrmts expected of the various SOS services (IOOS SOS 1.0, NDBC):
# for fmt in reversed(oFrmts):
for fmt in oFrmts:
try:
sml_recs, sml_errors = sos_collector.metadata_plus_exceptions(
output_format=fmt, timeout=200)
# if no valid SensorML docs returned, try next oFrmt:
if not sml_recs:
continue
else:
# assign correct DescribeSensor url (use sos_collector.feature rather than sml_recs.keys() to
# create DescribeSensor URLs for failures to record in logs):
for station in sos_collector.features:
describe_sensor_url[
station] = self.generate_describe_sensor_url(
sosgc, procedure=station, oFrmt=fmt)
# report on errors returned from metadata_plus_exceptions:
if sml_errors:
if self.verbose:
for station, msg in iteritems(sml_errors):
self.log.write(
u"\nSOS DescribeSensor error returned for: {station}, skipping. Error msg: {msg}"
.format(station=station, msg=msg))
print(
"SOS DescribeSensor error returned for: {station}, skipping. Error msg: {msg}"
.format(station=station, msg=msg))
else:
self.log.write(
u"\nSuccess, no errors returned from DescribeSensor requests in service: {sos}"
.format(sos=sos_url_params))
print(
"Success, no errors returned from DescribeSensor requests in service: {sos}"
.format(sos=sos_url_params))
break
# ServiceException shouldn't be thrown by metadata_plus_exceptions function, but handle regardless by attempting next oFrmt:
except ServiceException as e:
continue
station_recs = []
failures = []
# generate Pandas DataFrame by populating 'station_recs' list by parsing SensorML strings:
for station_idx, station_urn in enumerate(station_urns):
if station_urns_sel is not None:
# iterate oFrmts items for describe_sensor request (first is IOOS SOS spec-compliant, second is for NDBC SOS):
for fmt in oFrmts:
try:
describe_sensor_url[
station_urn] = self.generate_describe_sensor_url(
sosgc, procedure=station_urn, oFrmt=fmt)
sml_str = sosgc.describe_sensor(procedure=station_urn,
outputFormat=fmt,
timeout=200)
break
except ServiceException as e:
sml_errors[station_urn] = str(e)
continue
sml = SensorML(sml_str)
else:
# process valid SensorML responses, quietly pass on invalid stations (add to failures list for verbose reporting):
try:
sml = sml_recs[station_urn]
except KeyError:
self.log.write(
u"\n\nStation: {station} failed (no SensorML in sml_recs dict). URL: {ds}"
.format(station=station_urn,
ds=describe_sensor_url[station_urn].replace(
"&", "&")))
print(
"Station: {station} failed (no SensorML in sml_recs dict). URL: {ds}"
.format(station=station_urn,
ds=describe_sensor_url[station_urn].replace(
"&", "&")))
failures.append(station_urn)
continue
if self.sos_type.lower() == 'ndbc':
# later: add an error check
sosgc_station_offering = sosgc.contents[
'station-' + station_urn.split(':')[-1]]
else:
sosgc_station_offering = None
try:
ds = IoosDescribeSensor(sml._root)
except AttributeError:
self.log.write(
u"\nInvalid SensorML passed to IoosDescribeSensor. Check DescribeSensor request for : {station}, URL: "
.format(station=station,
ds=describe_sensor_url[station_urn].replace(
"&", "&")))
print(
"Invalid SensorML passed to IoosDescribeSensor. Check DescribeSensor request for : {station}, URL: "
.format(station=station,
ds=describe_sensor_url[station_urn].replace(
"&", "&")))
station = OrderedDict()
# debug:
if self.verbose:
self.log.write(u"\n\nProcessing station: {station}".format(
station=station_urn))
print("Processing station: {station}".format(
station=station_urn))
self.log.write("\n" +
etree.tostring(sml._root).decode('utf-8'))
# assign 'pos' to GML point location (accommodate 'gml:coordinates' as used by NDBC if gml:Point not found):
try:
pos = testXMLValue(ds.system.location.find(self.nsp('gml:Point/gml:pos'))) \
if testXMLValue(ds.system.location.find(self.nsp('gml:Point/gml:pos'))) is not None \
else testXMLValue(ds.system.location.find(self.nsp('gml:Point/gml:coordinates')))
station['lon'] = float(pos.split()[1])
station['lat'] = float(pos.split()[0])
except AttributeError as e:
station['lon'] = None
station['lat'] = None
system_el = sml._root.findall(self.nsp('sml:member'))[0].find(
self.nsp('sml:System'))
# Parse the DocumentList into a dict storing documents by index value 'name' (may cause index duplication
# errors but there is not enough information in SensorML for alternatives)
# Assume that member corresponds to xlink:arcrole="urn:ogc:def:role:webPage"
documents = system_el.findall(
self.nsp('sml:documentation/sml:DocumentList/sml:member'))
documents_dct = {}
for d in documents:
document = Documentation(d)
name = testXMLAttribute(d, "name")
# url = document.documents[0].url
documents_dct[name] = document
# obtain list of contacts (accommodate 'sml:contact' element repetition used by NDBC insead of ContactList):
contacts = system_el.findall(self.nsp('sml:contact/sml:ContactList/sml:member')) \
if system_el.findall(self.nsp('sml:contact/sml:ContactList/sml:member')) \
else system_el.findall(self.nsp('sml:contact'))
contacts_dct = {}
for c in contacts:
contact = Contact(c)
role = contact.role.split('/')[-1]
contacts_dct[role] = contact
# verify a 'publisher' Contact exists (template expects one):
if "publisher" not in contacts_dct.keys():
self.log.write(
u"\n\nStation: {station} skipped. No \'http://mmisw.org/ont/ioos/definition/publisher\' Contact role defined in SensorML as required. Roles defined: [{roles}]"
.format(station=station_urn,
roles=", ".join(contacts_dct.keys())))
print(
"Station: {station} skipped. No \'http://mmisw.org/ont/ioos/definition/publisher\' Contact role defined in SensorML as required. Roles defined: [{roles}]"
.format(station=station_urn,
roles=", ".join(contacts_dct.keys())))
failures.append(station_urn)
continue
sweQuants = system_el.findall(
self.nsp('sml:outputs/sml:OutputList/sml:output/swe:Quantity'))
quant_lst = [
sweQuant.attrib['definition'] for sweQuant in sweQuants
]
parameter_lst = [sweQuant.split('/')[-1] for sweQuant in quant_lst]
# attempt to read beginPosition, if available, otherwise use current date
# bc ISO requires date value in output location in template:
beginPosition = testXMLValue(
system_el.find(
self.nsp(
'sml:validTime/gml:TimePeriod/gml:beginPosition')))
try:
begin_service_date = parser.parse(beginPosition)
except (AttributeError, TypeError) as e:
begin_service_date = datetime.now(pytz.utc)
station['station_urn'] = station_urn
station['sos_url'] = sos_url_params
station['describesensor_url'] = describe_sensor_url[station_urn]
station['shortName'] = ds.shortName
station['longName'] = ds.longName
if self.sos_type.lower() == 'ndbc':
station['wmoID'] = station_urn.split(':')[-1]
else:
station['wmoID'] = ds.get_ioos_def('wmoID', 'identifier', ont)
station['serverName'] = self.server_name
# Some capabilities-level metadata:
station['title'] = sosgc.identification.title
station['abstract'] = sosgc.identification.abstract
station['keywords'] = sosgc.identification.keywords
station['begin_service_date'] = begin_service_date
# Beware that a station can have >1 classifier of the same type
# This code does not accommodate that possibility
station['platformType'] = ds.platformType
station['parentNetwork'] = ds.get_ioos_def('parentNetwork',
'classifier', ont)
station['sponsor'] = ds.get_ioos_def('sponsor', 'classifier', ont)
# store some nested dictionaries in 'station' for appropriate SensorML sources:
station['contacts_dct'] = contacts_dct
station['documents_dct'] = documents_dct
if self.sos_type.lower(
) == 'ndbc' and sosgc_station_offering is not None:
station['starting'] = sosgc_station_offering.begin_position
station['ending'] = sosgc_station_offering.end_position
else:
station['starting'] = ds.starting
station['ending'] = ds.ending
if self.sos_type.lower(
) == 'ndbc' and sosgc_station_offering is not None:
station[
'variable_uris'] = sosgc_station_offering.observed_properties
station['variables'] = [
var.split('/')[-1]
for var in sosgc_station_offering.observed_properties
]
station['parameter_uris'] = ','.join(station['variable_uris'])
station['parameters'] = ','.join(station['variables'])
else:
station['variable_uris'] = ds.variables
station['variables'] = [
var.split('/')[-1] for var in ds.variables
]
station['parameter_uris'] = ','.join(quant_lst)
station['parameters'] = ','.join(parameter_lst)
if self.verbose:
for var in station['variable_uris']:
self.log.write(u"\nvariable: {var}".format(var=var))
print("variable: {var}".format(var=var))
# print(sosgc.contents)
# for id, offering in sosgc.contents.iteritems():
# print("sosgc.contents: {item}".format(item=id))
# parse 'responseFormat' vals from SensorML:
# response_formats = sosgc.contents[station_urn].response_formats
response_formats = []
for id, sosgc.content in sosgc.contents.items():
if sosgc.content.name == station_urn:
response_formats = sosgc.content.response_formats
# response_formats = [ sosgc.content.response_formats for id, sosgc.content in sosgc.contents.items()
# if sosgc.content.name == station_urn ]
# match responseFormats from SensorML (response_formats) against those passed in --response_formats parameter to
# populate 'download_formats' list, that is then used to generate GetObservation requests for the template:
# (default --response_formats values are: 'application/json,application/zip; subtype=x-netcdf' )
download_formats = [
response_format for response_format in response_formats
if response_format in self.response_formats
]
station['response_formats'] = response_formats
station['download_formats'] = download_formats
if self.verbose:
for format in response_formats:
self.log.write(
u"\nresponseFormat: {format}".format(format=format))
print("responseFormat: {format}".format(format=format))
for format in download_formats:
self.log.write(
u"\ndownloadFormats: {format}".format(format=format))
print("downloadFormats: {format}".format(format=format))
# calculate event_time using self.getobs_req_hours:
event_time_formatstr = "{begin:%Y-%m-%dT%H:%M:%S}{utc_code}/{end:%Y-%m-%dT%H:%M:%S}{utc_code}"
utc_code = 'Z' if self.sos_type.lower() == 'ndbc' else None
if station['starting'] is not None and station[
'ending'] is not None:
event_time = event_time_formatstr.format(
begin=station['ending'] -
timedelta(hours=self.getobs_req_hours),
end=station['ending'],
utc_code=utc_code)
if self.verbose:
self.log.write(
u"\nUsing starting/ending times from SensorML for eventTime"
)
print(
"Using starting/ending times from SensorML for eventTime"
)
self.log.write(
u"\nobservationTimeRange: starting: {start}, ending: {end}"
.format(start=station['starting'],
end=station['ending']))
print(
"observationTimeRange: starting: {start}, ending: {end}"
.format(start=station['starting'],
end=station['ending']))
else:
now = datetime.now(pytz.utc)
then = now - timedelta(hours=self.getobs_req_hours)
event_time = event_time_formatstr.format(begin=then,
end=now,
utc_code=utc_code)
if self.verbose:
self.log.write(
u"\nNo 'observationTimeRange' present in SensorML. Using present time for eventTime: then: {then:%Y-%m-%dT%H:%M:%S%z}, now: {now:%Y-%m-%dT%H:%M:%S%z}"
.format(then=then, now=now))
print(
"No 'observationTimeRange' present in SensorML. Using present time for eventTime: then: {then:%Y-%m-%dT%H:%M:%S%z}, now: {now:%Y-%m-%dT%H:%M:%S%z}"
.format(then=then, now=now))
if self.verbose:
self.log.write(u"\neventTime: {time}".format(time=event_time))
print("eventTime: {time}".format(time=event_time))
# create a dict to store parameters for valid example GetObservation requests for station:
getobs_req_dct = {}
# populate a parameters dictionary for download links for each 'observedProperty' type
# and secondly for each 'responseFormat' per observedProperty:
getobs_params_base = {
'service': 'SOS',
'request': 'GetObservation',
'version': '1.0.0',
'offering': station_urn,
'eventTime': event_time
}
for variable in station['variable_uris']:
getobs_params = getobs_params_base.copy()
getobs_params['observedProperty'] = variable
variable = variable.split('/')[-1]
for format in download_formats:
getobs_params['responseFormat'] = format
getobs_request_url_encoded = sos_url + '?' + urlencode(
getobs_params)
getobs_request_url = unquote(getobs_request_url_encoded)
getobs_req_dct[variable + '-' + format] = {
'variable':
variable,
'url':
getobs_request_url,
'format_type':
self.RESPONSE_FORMAT_TYPE_MAP.get(format, format),
'format_name':
self.RESPONSE_FORMAT_NAME_MAP.get(format, format)
}
if self.verbose:
self.log.write(
u"\ngetobs_request_url (var: {variable}): {getobs_request_url}"
.format(variable=variable.split("/")[-1],
getobs_request_url=getobs_request_url))
print(
"getobs_request_url (var: {variable}): {getobs_request_url}"
.format(variable=variable.split("/")[-1],
getobs_request_url=getobs_request_url))
# ToDo: finish adding the 'getobs_req_dct' to the output template
station['getobs_req_dct'] = getobs_req_dct
station_recs.append(station)
# extra debug for failed stations in verbose mode:
if self.verbose:
self.log.write(
u"\n\n\nSOS DescribeSensor request errors recap. Failed requests:"
)
print("SOS DescribeSensor request errors recap. Failed requests:")
for station_fail, msg in iteritems(sml_errors):
self.log.write(
u"\n{station} - {msg}. DescribeSensor URL: {ds}".format(
station=station_fail,
msg=msg,
ds=describe_sensor_url[station_fail].replace(
"&", "&")))
print("{station} - {msg}. DescribeSensor URL: {ds}".format(
station=station_fail,
msg=msg,
ds=describe_sensor_url[station_fail].replace("&",
"&")))
if failures:
self.log.write(
u"\nStations in 'failures' list (should match DescribeSensor errors):"
)
print(
"Stations in 'failures' list (should match DescribeSensor errors):"
)
for station_fail in failures:
self.log.write(u"\n{station}".format(station=station_fail))
print("{station}".format(station=station_fail))
if station_recs:
stations_df = pd.DataFrame.from_records(station_recs,
columns=station.keys())
stations_df.index = stations_df['station_urn']
return stations_df
else:
return None
class SosHarvest(Harvester):
def __init__(self, service):
Harvester.__init__(self, service)
def harvest(self):
self.sos = SensorObservationService(self.service.get('url'))
for offering in self.sos.offerings:
# TODO: We assume an offering should only have one procedure here
# which will be the case in sos 2.0, but may not be the case right now
# on some non IOOS supported servers.
uid = offering.procedures[0]
sp_uid = uid.split(":")
# List storing the stations that have already been processed in this SOS server.
# This is kept and checked later to avoid servers that have the same stations in many offerings.
processed = []
# temnplate: urn:ioos:type:authority:id
# sample: ioos:station:wmo:21414
if sp_uid[2] == "station": # Station Offering
if not uid in processed:
self.process_station(uid)
processed.append(uid)
elif sp_uid[2] == "network": # Network Offering
network_ds = IoosDescribeSensor(
self.sos.describe_sensor(
outputFormat=
'text/xml;subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"',
procedure=uid))
# Iterate over stations in the network and process them individually
for proc in network_ds.procedures:
if proc is not None and proc.split(":")[2] == "station":
if not proc in processed:
self.process_station(proc)
processed.append(proc)
def process_station(self, uid):
""" Makes a DescribeSensor request based on a 'uid' parameter being a station procedure """
GML_NS = "http://www.opengis.net/gml"
XLINK_NS = "http://www.w3.org/1999/xlink"
with app.app_context():
metadata_value = etree.fromstring(
self.sos.describe_sensor(
outputFormat=
'text/xml;subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"',
procedure=uid))
station_ds = IoosDescribeSensor(metadata_value)
unique_id = station_ds.id
if unique_id is None:
app.logger.warn(
"Could not get a 'stationID' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/stationID'"
)
return
dataset = db.Dataset.find_one({'uid': unicode(unique_id)})
if dataset is None:
dataset = db.Dataset()
dataset.uid = unicode(unique_id)
# Find service reference in Dataset.services and remove (to replace it)
tmp = dataset.services[:]
for d in tmp:
if d['service_id'] == self.service.get('_id'):
dataset.services.remove(d)
# Parsing messages
messages = []
# NAME
name = unicode_or_none(station_ds.shortName)
if name is None:
messages.append(
u"Could not get a 'shortName' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/shortName'"
)
# DESCRIPTION
description = unicode_or_none(station_ds.longName)
if description is None:
messages.append(
u"Could not get a 'longName' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/longName'"
)
# PLATFORM TYPE
asset_type = unicode_or_none(station_ds.platformType)
if asset_type is None:
messages.append(
u"Could not get a 'platformType' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/platformType'"
)
# LOCATION is in GML
gj = None
loc = station_ds.location
if loc is not None and loc.tag == "{%s}Point" % GML_NS:
pos_element = loc.find("{%s}pos" % GML_NS)
# strip out points
positions = map(float, testXMLValue(pos_element).split(" "))
crs = Crs(testXMLAttribute(pos_element, "srsName"))
if crs.axisorder == "yx":
gj = json.loads(
geojson.dumps(
geojson.Point([positions[1], positions[0]])))
else:
gj = json.loads(
geojson.dumps(
geojson.Point([positions[0], positions[1]])))
else:
messages.append(
u"Found an unrecognized child of the sml:location element and did not attempt to process it: %s"
% etree.tostring(loc).strip())
service = {
# Reset service
'name': name,
'description': description,
'service_type': self.service.get('service_type'),
'service_id': ObjectId(self.service.get('_id')),
'data_provider': self.service.get('data_provider'),
'metadata_type': u'sensorml',
'metadata_value':
unicode(etree.tostring(metadata_value)).strip(),
'messages': map(unicode, messages),
'keywords': map(unicode, sorted(station_ds.keywords)),
'variables': map(unicode, sorted(station_ds.variables)),
'asset_type': asset_type,
'geojson': gj,
'updated': datetime.utcnow()
}
dataset.services.append(service)
dataset.updated = datetime.utcnow()
dataset.save()
return "Harvested"
# Accessing ncSOS with OWSLib # <codecell> from owslib.sos import SensorObservationService import pdb from owslib.etree import etree import pandas as pd import datetime as dt # <codecell> # usgs woods hole # buoy data (ADCP) url='http://geoport.whoi.edu/thredds/sos/usgs/data2/emontgomery/stellwagen/CF-1.6/HURRIRENE_BB/9141wh-a.nc' usgs = SensorObservationService(url) contents = usgs.contents # <codecell> usgs.contents # <codecell> off = usgs.offerings[1] off.name # <codecell> off.response_formats
class IoosSweSos(Collector):
def __init__(self, url, xml=None):
super(IoosSweSos, self).__init__()
self.server = Sos(url, xml=xml)
def metadata(self, output_format=None, feature_name_callback=None, **kwargs):
"""
Gets SensorML objects for all procedures in your filtered features.
You should override the default output_format for servers that do not
respond properly.
"""
callback = feature_name_callback or str
if output_format is None:
output_format = 'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"'
responses = []
if self.features is not None:
for feature in self.features:
ds_kwargs = kwargs.copy()
ds_kwargs.update({'outputFormat': output_format,
'procedure' : callback(feature)})
responses.append(SensorML(self.server.describe_sensor(**ds_kwargs)))
return responses
def setup_params(self, **kwargs):
params = kwargs
if self.bbox is not None:
params["featureOfInterest"] = "BBOX:%s,%s,%s,%s" % (self.bbox[0], self.bbox[1], self.bbox[2], self.bbox[3])
if self.start_time is not None:
params["eventTime"] = self.start_time.strftime('%Y-%m-%dT%H:%M:%SZ')
if self.end_time is not None:
params["eventTime"] += "/%s" % self.end_time.strftime('%Y-%m-%dT%H:%M:%SZ')
if self.variables is None or len(self.variables) < 1:
raise ValueError("You must set a filter for at least one variable (observedProperty)")
else:
ops = ",".join(self.variables)
if isinstance(ops, basestring):
ops = [ops]
params["observedProperties"] = ops
return params
def collect(self, **kwargs):
# there is an unfortunate difference in how 52N and ncSOS handle the response format.
# 52N expects subtype, ncSOS expects schema.
# consult the observed properties and getcaps to figure out which should be used if none passed
if 'responseFormat' not in kwargs:
# iterate offerings and see if we need to change to subtype
off_dict = {off.name : off for off in self.server.offerings}
response_format = None
for offering in kwargs.get('offerings', []):
if offering not in off_dict:
continue
ioos_formats = [rf for rf in off_dict[offering].response_formats if 'ioos_sos/1.0' in rf]
if not len(ioos_formats):
raise StandardError("No ioos_sos/1.0 response format found for offering %s" % offering)
if response_format != ioos_formats[0]:
response_format = ioos_formats[0]
kwargs["responseFormat"] = response_format
return IoosGetObservation(self.raw(**kwargs)).observations
def raw(self, **kwargs):
params = self.setup_params(**kwargs)
return self.server.get_observation(**params)
class SosHarvest(Harvester):
def __init__(self, service):
Harvester.__init__(self, service)
def harvest(self):
self.sos = SensorObservationService(self.service.get('url'))
for offering in self.sos.offerings:
# TODO: We assume an offering should only have one procedure here
# which will be the case in sos 2.0, but may not be the case right now
# on some non IOOS supported servers.
uid = offering.procedures[0]
sp_uid = uid.split(":")
# List storing the stations that have already been processed in this SOS server.
# This is kept and checked later to avoid servers that have the same stations in many offerings.
processed = []
# temnplate: urn:ioos:type:authority:id
# sample: ioos:station:wmo:21414
if sp_uid[2] == "station": # Station Offering
if not uid in processed:
self.process_station(uid)
processed.append(uid)
elif sp_uid[2] == "network": # Network Offering
network_ds = IoosDescribeSensor(self.sos.describe_sensor(outputFormat='text/xml;subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"', procedure=uid))
# Iterate over stations in the network and process them individually
for proc in network_ds.procedures:
if proc is not None and proc.split(":")[2] == "station":
if not proc in processed:
self.process_station(proc)
processed.append(proc)
def process_station(self, uid):
""" Makes a DescribeSensor request based on a 'uid' parameter being a station procedure """
GML_NS = "http://www.opengis.net/gml"
XLINK_NS = "http://www.w3.org/1999/xlink"
with app.app_context():
metadata_value = etree.fromstring(self.sos.describe_sensor(outputFormat='text/xml;subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"', procedure=uid))
station_ds = IoosDescribeSensor(metadata_value)
unique_id = station_ds.id
if unique_id is None:
app.logger.warn("Could not get a 'stationID' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/stationID'")
return
dataset = db.Dataset.find_one( { 'uid' : unicode(unique_id) } )
if dataset is None:
dataset = db.Dataset()
dataset.uid = unicode(unique_id)
# Find service reference in Dataset.services and remove (to replace it)
tmp = dataset.services[:]
for d in tmp:
if d['service_id'] == self.service.get('_id'):
dataset.services.remove(d)
# Parsing messages
messages = []
# NAME
name = unicode_or_none(station_ds.shortName)
if name is None:
messages.append(u"Could not get a 'shortName' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/shortName'")
# DESCRIPTION
description = unicode_or_none(station_ds.longName)
if description is None:
messages.append(u"Could not get a 'longName' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/longName'")
# PLATFORM TYPE
asset_type = unicode_or_none(station_ds.platformType)
if asset_type is None:
messages.append(u"Could not get a 'platformType' from the SensorML identifiers. Looking for a definition of 'http://mmisw.org/ont/ioos/definition/platformType'")
# LOCATION is in GML
gj = None
loc = station_ds.location
if loc is not None and loc.tag == "{%s}Point" % GML_NS:
pos_element = loc.find("{%s}pos" % GML_NS)
# strip out points
positions = map(float, testXMLValue(pos_element).split(" "))
crs = Crs(testXMLAttribute(pos_element, "srsName"))
if crs.axisorder == "yx":
gj = json.loads(geojson.dumps(geojson.Point([positions[1], positions[0]])))
else:
gj = json.loads(geojson.dumps(geojson.Point([positions[0], positions[1]])))
else:
messages.append(u"Found an unrecognized child of the sml:location element and did not attempt to process it: %s" % etree.tostring(loc).strip())
service = {
# Reset service
'name' : name,
'description' : description,
'service_type' : self.service.get('service_type'),
'service_id' : ObjectId(self.service.get('_id')),
'data_provider' : self.service.get('data_provider'),
'metadata_type' : u'sensorml',
'metadata_value' : unicode(etree.tostring(metadata_value)).strip(),
'messages' : map(unicode, messages),
'keywords' : map(unicode, sorted(station_ds.keywords)),
'variables' : map(unicode, sorted(station_ds.variables)),
'asset_type' : asset_type,
'geojson' : gj,
'updated' : datetime.utcnow()
}
dataset.services.append(service)
dataset.updated = datetime.utcnow()
dataset.save()
return "Harvested"
def get_stations_df(self, sos_url, station_urns_sel=None):
""" Returns a GeoDataFrame
"""
# LATER: ADD ERROR TEST/CATCH AFTER EACH WEB REQUEST
oFrmt = 'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"'
params = {
'service': 'SOS',
'request': 'GetCapabilities',
'acceptVersions': '1.0.0'
}
sos_url_params = sos_url + '?' + urlencode(params)
sos_url_params_esc = sos_url_params.replace("&", "&")
# sos_url_params_quoted = quote(sos_url_params,"/=:")
# sos_url_params_unquoted = unquote(sos_url_params)
try:
sosgc = SensorObservationService(sos_url_params)
except (ConnectionError, ReadTimeout) as e:
self.log.write(
u"Error: unable to connect to SOS service: {url} due to HTTP connection error.\n"
.format(url=sos_url_params))
self.log.write(
u"HTTP connection error: {err}.\n".format(err=e.message))
sys.exit(
"Error: unable to connect to SOS service: {url}. \nUnderlying HTTP connection error: {err}"
.format(url=sos_url_params, err=e.message))
if station_urns_sel is not None:
station_urns = station_urns_sel
else:
sos_collector = IoosSweSos(sos_url)
station_urns = [
urn.name for urn in sos_collector.server.offerings
if 'network' not in urn.name.split(':')
]
sos_collector.features = station_urns
sml_lst = sos_collector.metadata(timeout=200)
station_recs = []
for station_idx, station_urn in enumerate(station_urns):
if station_urns_sel is not None:
sml_str = sosgc.describe_sensor(procedure=station_urn,
outputFormat=oFrmt,
timeout=200)
sml = SensorML(sml_str)
else:
sml = sml_lst[station_idx]
# debug:
# if self.verbose:
# self.log.write(unicode(etree.tostring(sml._root)))
ds = IoosDescribeSensor(sml._root)
pos = testXMLValue(
ds.system.location.find(self.nsp('gml:Point/gml:pos')))
system_el = sml._root.findall(self.nsp('sml:member'))[0].find(
self.nsp('sml:System'))
# Parse the DocumentList into a dict storing documents by index value 'name' (may cause index duplication
# errors but there is not enough information in SensorML for alternatives)
# Assume that member corresponds to xlink:arcrole="urn:ogc:def:role:webPage"
documents = system_el.findall(
self.nsp('sml:documentation/sml:DocumentList/sml:member'))
documents_dct = {}
for d in documents:
document = Documentation(d)
name = testXMLAttribute(d, "name")
# url = document.documents[0].url
documents_dct[name] = document
contacts = system_el.findall(
self.nsp('sml:contact/sml:ContactList/sml:member'))
contacts_dct = {}
for c in contacts:
contact = Contact(c)
role = contact.role.split('/')[-1]
contacts_dct[role] = contact
sweQuants = system_el.findall(
self.nsp('sml:outputs/sml:OutputList/sml:output/swe:Quantity'))
quant_lst = [
sweQuant.attrib['definition'] for sweQuant in sweQuants
]
parameter_lst = [sweQuant.split('/')[-1] for sweQuant in quant_lst]
# attempt to read beginPosition, if available:
beginPosition = testXMLValue(
system_el.find(
self.nsp(
'sml:validTime/gml:TimePeriod/gml:beginPosition')))
try:
begin_service_date = parser.parse(beginPosition)
except AttributeError as e:
begin_service_date = None
station = OrderedDict()
station['station_urn'] = station_urn
station['sos_url'] = sos_url_params_esc
station['lon'] = float(pos.split()[1])
station['lat'] = float(pos.split()[0])
station['shortName'] = ds.shortName
station['longName'] = ds.longName
station['wmoID'] = ds.get_ioos_def('wmoID', 'identifier', ont)
station['serverName'] = self.server_name
# Some capabilities-level metadata:
station['title'] = sosgc.identification.title
station['abstract'] = sosgc.identification.abstract
station['keywords'] = sosgc.identification.keywords
station['begin_service_date'] = begin_service_date
# Beware that a station can have >1 classifier of the same type
# This code does not accommodate that possibility
station['platformType'] = ds.platformType
station['parentNetwork'] = ds.get_ioos_def('parentNetwork',
'classifier', ont)
station['sponsor'] = ds.get_ioos_def('sponsor', 'classifier', ont)
# store some nested dictionaries in 'station' for appopriate SensorML sources:
station['contacts_dct'] = contacts_dct
station['documents_dct'] = documents_dct
# MW: the 'operator_' and 'publisher_' attributes can be removed bc they are not used
# in the template code currently in favor of 'contacts_dct'
# station['operatorSector'] = ds.get_ioos_def('operatorSector', 'classifier', ont)
# station['operator_org'] = contacts_dct['operator'].organization
# station['operator_country'] = contacts_dct['operator'].country
# station['operator_url'] = contacts_dct['operator'].url
# station['operator_email'] = contacts_dct['operator'].email
# station['publisher'] = ds.get_ioos_def('publisher', 'classifier', ont)
# station['publisher_org'] = contacts_dct['publisher'].organization
# station['publisher_url'] = contacts_dct['publisher'].url
# station_dct['publisher_email'] = contacts_dct['publisher'].electronicMailAddress
station['starting'] = ds.starting
station['ending'] = ds.ending
# station['starting_isostr'] = datetime.isoformat(ds.starting)
# station['ending_isostr'] = datetime.isoformat(ds.ending)
station['parameter_uris'] = ','.join(quant_lst)
station['parameters'] = ','.join(parameter_lst)
station['variables'] = [var.split('/')[-1] for var in ds.variables]
# debug:
if self.verbose:
self.log.write(u"\nProcessing station: {station}\n".format(
station=station_urn))
print("\nProcessing station: {station}".format(
station=station_urn))
for var in ds.variables:
self.log.write(u"variable: {var}\n".format(var=var))
print("variable: {var}".format(var=var))
# print(sosgc.contents)
# for id, offering in sosgc.contents.iteritems():
# print("sosgc.contents: {item}".format(item=id))
# parse 'responseFormat' values and populate list:
# response_formats = sosgc.contents[station_urn].response_formats
response_formats = []
for id, sosgc.content in sosgc.contents.items():
if sosgc.content.name == station_urn:
response_formats = sosgc.content.response_formats
# response_formats = [ sosgc.content.response_formats for id, sosgc.content in sosgc.contents.items() if sosgc.content.name == station_urn ]
# subset responseFormats (response_formats) for download links matching those passed in --response_formats parameter
# (or 'application/json,application/zip; subtype=x-netcdf' by default):
download_formats = [
response_format for response_format in response_formats
if response_format in self.response_formats
]
station['response_formats'] = response_formats
station['download_formats'] = download_formats
if self.verbose:
for format in response_formats:
self.log.write(
u"responseFormat: {format}\n".format(format=format))
print("responseFormat: {format}".format(format=format))
for format in download_formats:
self.log.write(
u"downloadFormats: {format}\n".format(format=format))
print("downloadFormats: {format}".format(format=format))
# calculate event_time using self.getobs_req_hours:
if ds.starting is not None and ds.ending is not None:
event_time = "{begin:%Y-%m-%dT%H:%M:%S}/{end:%Y-%m-%dT%H:%M:%S}\n".format(
begin=ds.ending - timedelta(hours=self.getobs_req_hours),
end=ds.ending)
else:
now = datetime.now(pytz.utc)
then = now - timedelta(hours=self.getobs_req_hours)
event_time = "{begin:%Y-%m-%dT%H:%M:%S}/{end:%Y-%m-%dT%H:%M:%S}\n".format(
begin=then, end=now)
if self.verbose:
self.log.write(
u"then: {then:%Y-%m-%dT%H:%M:%S%z}, now: {now:%Y-%m-%dT%H:%M:%S%z}\n"
.format(then=then, now=now))
print(
"then: {then:%Y-%m-%dT%H:%M:%S%z}, now: {now:%Y-%m-%dT%H:%M:%S%z}"
.format(then=then, now=now))
if self.verbose:
self.log.write(u"eventTime: {time}\n".format(time=event_time))
print("eventTime: {time}".format(time=event_time))
# create a dict to store parameters for valid example GetObservation requests for station:
getobs_req_dct = {}
# populate a parameters dictionary for download links for each 'observedProperty' type and secondly for each 'responseFormat' per observedProperty:
getobs_params_base = {
'service': 'SOS',
'request': 'GetObservation',
'version': '1.0.0',
'offering': station_urn,
'eventTime': event_time
}
for variable in ds.variables:
getobs_params = getobs_params_base.copy()
getobs_params['observedProperty'] = variable
variable = variable.split('/')[-1]
for format in download_formats:
getobs_params['responseFormat'] = format
getobs_request_url_encoded = sos_url + '?' + urlencode(
getobs_params)
getobs_request_url = unquote(getobs_request_url_encoded)
getobs_request_url_esc = getobs_request_url.replace(
"&", "&")
getobs_req_dct[variable + '-' + format] = {
'variable': variable,
'url': getobs_request_url_esc,
'format_type': self.RESPONSE_FORMAT_TYPE_MAP[format],
'format_name': self.RESPONSE_FORMAT_NAME_MAP[format]
}
if self.verbose:
self.log.write(
u"getobs_request_url (var: {variable}): {getobs_request_url}\ngetobs_request_url_esc (var: {variable}): {getobs_request_url_esc}\n"
.format(
variable=variable.split("/")[-1],
getobs_request_url=getobs_request_url,
getobs_request_url_esc=getobs_request_url_esc))
print(
"getobs_request_url (var: {variable}): {getobs_request_url}\ngetobs_request_url_esc (var: {variable}): {getobs_request_url_esc}"
.format(
variable=variable.split("/")[-1],
getobs_request_url=getobs_request_url,
getobs_request_url_esc=getobs_request_url_esc))
# ToDo: finish adding the 'getobs_req_dct' to the output template
station['getobs_req_dct'] = getobs_req_dct
station_recs.append(station)
stations_df = pd.DataFrame.from_records(station_recs,
columns=station.keys())
stations_df.index = stations_df['station_urn']
return stations_df
# <codecell> from owslib.sos import SensorObservationService from owslib.etree import etree import pandas as pd import datetime as dt import matplotlib.pyplot as plt import numpy as np %matplotlib inline # <codecell> # usgs woods hole # regular time series data url='http://geoport.whoi.edu/thredds/sos/usgs/data2/emontgomery/stellwagen/CF-1.6/BUZZ_BAY/2651-A.cdf' usgs = SensorObservationService(url) contents = usgs.contents # <codecell> usgs.contents # <codecell> off = usgs.offerings[1] off.name # <codecell> off.response_formats
def test_sos_caps():
sos = SensorObservationService(SERVICE_URL)
assert str(sos.contents['81102 - PM10']) == "Offering id: 81102 - PM10, name: Particulate Matter < 10 µm"
assert repr(sos.contents['81102 - PM10']) == "<SosObservationOffering 'Particulate Matter < 10 µm'>"
def __init__(self, url, xml=None):
super(IoosSweSos, self).__init__()
self.server = Sos(url, xml=xml)
# But can we formulate, request and process this same query (and others like it) using OWSlib?
# In[64]:
get_ipython().magic('matplotlib inline')
from owslib.sos import SensorObservationService
import pdb
from owslib.etree import etree
import pandas as pd
import datetime as dt
import numpy as np
# In[46]:
url = 'http://sdf.ndbc.noaa.gov/sos/server.php?request=GetCapabilities&service=SOS&version=1.0.0'
ndbc = SensorObservationService(url)
# In[47]:
# usgs woods hole
# buoy data (single current meter)
url = 'http://geoport-dev.whoi.edu/thredds/sos/usgs/data2/notebook/1211-AA.cdf'
usgs = SensorObservationService(url)
contents = usgs.contents
# In[48]:
usgs.contents
# In[49]:
