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 test_sensor(self):
data = open(resource_file(os.path.join('ioos_swe','SML-DescribeSensor-Sensor.xml')), "rU").read()
d = IoosDescribeSensor(data)
assert d.ioos_version == "1.0"
assert d.system.name == "urn:ioos:sensor:us.glos:45023:sea_water_temperature"
assert d.starting == datetime(2013, 8, 26, 18, 10, tzinfo=pytz.utc)
assert d.ending == datetime(2013, 8, 26, 18, 10, tzinfo=pytz.utc)
def test_network(self):
data = open(resource_file(os.path.join('ioos_swe','SML-DescribeSensor-Network.xml')), "rU").read()
d = IoosDescribeSensor(data)
assert d.ioos_version == "1.0"
assert d.system.name == "urn:ioos:network:nanoos:all"
assert d.procedures == sorted([u'urn:ioos:station:wmo:41001', u'urn:ioos:station:wmo:41002'])
assert d.starting == datetime(2008, 4, 28, 8, tzinfo=pytz.utc)
assert d.ending == datetime(2012, 12, 27, 19, tzinfo=pytz.utc)
def test_station(self):
data = open(resource_file(os.path.join('ioos_swe','SML-DescribeSensor-Station.xml')), "rU").read()
d = IoosDescribeSensor(data)
assert d.ioos_version == "1.0"
assert d.system.name == "urn:ioos:station:wmo:41001"
assert d.variables == sorted([u'http://mmisw.org/ont/cf/parameter/sea_water_temperature',
u'http://mmisw.org/ont/cf/parameter/sea_water_salinity',
u'http://mmisw.org/ont/cf/parameter/air_pressure',
u'http://mmisw.org/ont/cf/parameter/air_temperature'])
assert d.starting == datetime(2008, 4, 28, 8, tzinfo=pytz.utc)
assert d.ending == datetime(2012, 12, 27, 19, tzinfo=pytz.utc)
def harvest(self):
self.sos = SensorObservationService(self.service.get('url'))
scores = self.ccheck_service()
metamap = self.metamap_service()
try:
self.save_ccheck_service('ioos', scores, metamap)
finally:
#except Exception as e:
#app.logger.warn("could not save compliancecheck/metamap information: %s", e)
pass
# 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 = []
# handle network:all by increasing max timeout
net_len = len(self.sos.offerings)
net_timeout = 120 if net_len <= 36 else 5 * net_len
# allow searching child offerings for by name for network offerings
name_lookup = {o.name: o for o in self.sos.offerings}
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(":")
# template: urn:ioos:type:authority:id
# sample: ioos:station:wmo:21414
if len(sp_uid) > 2 and sp_uid[2] == "network": # Network Offering
if uid[-3:].lower() == 'all':
continue # Skip the all
net = self._describe_sensor(uid, timeout=net_timeout)
network_ds = IoosDescribeSensor(net)
# 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:
# offering associated with this procedure
proc_off = name_lookup.get(proc)
self.process_station(proc, proc_off)
processed.append(proc)
else:
# Station Offering, or malformed urn - try it anyway as if it is a station
if not uid in processed:
self.process_station(uid, offering)
processed.append(uid)
def process_station(self, uid, offering):
""" Makes a DescribeSensor request based on a 'uid' parameter being a
station procedure. Also pass along an offering with
getCapabilities information for items such as temporal extent"""
GML_NS = "http://www.opengis.net/gml"
XLINK_NS = "http://www.w3.org/1999/xlink"
with app.app_context():
app.logger.info("process_station: %s", uid)
desc_sens = self._describe_sensor(uid, timeout=1200)
# FIXME: add some kind of notice saying the station failed
if desc_sens is None:
app.logger.warn(
"Could not get a valid describeSensor response")
return
metadata_value = etree.fromstring(desc_sens)
sensor_ml = SensorML(metadata_value)
try:
station_ds = IoosDescribeSensor(metadata_value)
# if this doesn't conform to IOOS SensorML sub, fall back to
# manually picking apart the SensorML
except ows.ExceptionReport:
station_ds = process_sensorml(sensor_ml.members[0])
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)
dataset['active'] = True
# 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(
getattr(station_ds, 'platformType', None))
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)
# some older responses may uses the deprecated coordinates
# element
if pos_element is None:
# if pos not found use deprecated coordinates element
pos_element = loc.find("{%s}coordinates" % GML_NS)
# strip out points
positions = map(float, pos_element.text.split(" "))
for el in [pos_element, loc]:
srs_name = testXMLAttribute(el, "srsName")
if srs_name:
crs = Crs(srs_name)
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]])))
break
else:
if positions:
messages.append(
u"Position(s) found but could not parse SRS: %s, %s"
% (positions, srs_name))
else:
messages.append(
u"Found an unrecognized child of the sml:location element and did not attempt to process it: %s"
% loc)
meta_str = unicode(etree.tostring(metadata_value)).strip()
if len(meta_str) > 4000000:
messages.append(
u'Metadata document was too large to store (len: %s)' %
len(meta_str))
meta_str = u''
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': u'',
'time_min': getattr(offering, 'begin_position', None),
'time_max': getattr(offering, 'end_position', None),
'messages': map(unicode, messages),
'keywords': map(unicode, sorted(station_ds.keywords)),
'variables': map(unicode, sorted(station_ds.variables)),
'asset_type': get_common_name(asset_type),
'geojson': gj,
'updated': datetime.utcnow()
}
dataset.services.append(service)
dataset.updated = datetime.utcnow()
dataset.save()
# do compliance checker / metadata now
scores = self.ccheck_station(sensor_ml)
metamap = self.metamap_station(sensor_ml)
try:
self.save_ccheck_station('ioos', dataset._id, scores, metamap)
except Exception as e:
app.logger.warn(
"could not save compliancecheck/metamap information: %s",
e)
return "Harvest Successful"
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 ''
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
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