class IoosSweSosTest(unittest.TestCase): def setUp(self): # we have to pick SOS to test against, NANOOS it is: self.c = IoosSweSos("http://data.nanoos.org/52nsos/sos/kvp") # self.c.features = [urn.name for urn in self.c.server.offerings] @pytest.mark.xfail def test_server_id(self): assert ( self.c.server.identification.title == "NANOOS Sensor Observation Service (SOS), a 52North IOOS SOS server" ) assert self.c.server.identification.service == "OGC:SOS" assert self.c.server.identification.version == "1.0.0" assert self.c.server.identification.fees == "NONE" assert self.c.server.identification.accessconstraints == "NONE" @pytest.mark.xfail def test_metdata(self): self.c.features = ["urn:ioos:station:nanoos:apl_nemo"] response = self.c.metadata( output_format= 'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"') assert isinstance(response, list) assert isinstance(response[0], SensorML) @pytest.mark.xfail def test_metadata_plus_exceptions(self): self.c.features = ["urn:ioos:station:nanoos:apl_nemo"] response, failures = self.c.metadata_plus_exceptions( output_format= 'text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"') assert isinstance(response, dict) assert isinstance(failures, dict) assert isinstance(response[self.c.features[0]], SensorML)
class IoosSweSosTest(unittest.TestCase): def setUp(self): # we have to pick SOS to test against, NANOOS it is: self.c = IoosSweSos("http://data.nanoos.org/52nsos/sos/kvp") # self.c.features = [urn.name for urn in self.c.server.offerings] @pytest.mark.xfail def test_server_id(self): assert ( self.c.server.identification.title == "NANOOS Sensor Observation Service (SOS), a 52North IOOS SOS server" ) assert self.c.server.identification.service == "OGC:SOS" assert self.c.server.identification.version == "1.0.0" assert self.c.server.identification.fees == "NONE" assert self.c.server.identification.accessconstraints == "NONE" @pytest.mark.xfail def test_metdata(self): self.c.features = ["urn:ioos:station:nanoos:apl_nemo"] response = self.c.metadata( output_format='text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"' ) assert isinstance(response, list) assert isinstance(response[0], SensorML) @pytest.mark.xfail def test_metadata_plus_exceptions(self): self.c.features = ["urn:ioos:station:nanoos:apl_nemo"] response, failures = self.c.metadata_plus_exceptions( output_format='text/xml; subtype="sensorML/1.0.1/profiles/ioos_sos/1.0"' ) assert isinstance(response, dict) assert isinstance(failures, dict) assert isinstance(response[self.c.features[0]], SensorML)
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