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import isodate
from lxml import etree
from past.builtins import basestring
from ulmo import util
def parse_site_values(content_io, namespace, query_isodate=None, methods=None):
"""parses values out of a waterml file; content_io should be a file-like object"""
data_dict = {}
metadata_elements = [
# (element name, name of collection,
# key from element dict to use as for a key in the collections dict)
('censorCode', 'censor_codes', 'censor_code'),
('method', 'methods', 'id'),
('offset', 'offsets', 'id'),
('qualifier', 'qualifiers', 'id'),
('qualityControlLevel', 'quality_control_levels', 'id'),
('source', 'sources', 'id')
]
for (event, ele) in etree.iterparse(content_io):
if ele.tag == namespace + "timeSeries":
source_info_element = ele.find(namespace + 'sourceInfo')
site_info = _parse_site_info(source_info_element, namespace)
var_element = ele.find(namespace + 'variable')
variable = _parse_variable(var_element, namespace)
values_elements = ele.findall(namespace + 'values')
code = variable['code']
if isinstance(methods, basestring):
method = methods
elif isinstance(methods, dict):
method = methods.get(code, None)
else:
method = None
if 'statistic' in variable:
code += ":" + variable['statistic']['code']
if method is None:
if len(values_elements) > 1:
raise ValueError(
'found more than one method for %s. need to specify'
'specify code or "all".' % variable['code'])
values_element = values_elements[0]
values = _parse_values(values_element, namespace)
data_dict[code] = {
'site': site_info,
'variable': variable,
}
data_dict[code].update({'values': values})
metadata = _parse_metadata(
values_element, metadata_elements, namespace)
data_dict[code].update(metadata)
if query_isodate:
data_dict[code]['last_refresh'] = query_isodate
elif method == 'all':
for values_element in values_elements:
values = _parse_values(values_element, namespace)
metadata = _parse_metadata(
values_element, metadata_elements, namespace)
if len(values_elements) > 1:
updated_code = code + ':' + str(
list(metadata['methods'].values())[0]['id'])
else:
updated_code = code
data_dict[updated_code] = {
'site': site_info.copy(),
'variable': variable,
}
data_dict[updated_code].update({'values': values})
data_dict[updated_code].update(metadata)
if query_isodate:
data_dict[updated_code]['last_refresh'] = query_isodate
else:
for values_element in values_elements:
if values_element.find(
namespace + 'method[@methodID="%s"]' % method)\
is not None:
values = _parse_values(values_element, namespace)
metadata = _parse_metadata(
values_element, metadata_elements, namespace)
data_dict[code] = {
'site': site_info,
'variable': variable,
}
data_dict[code].update({'values': values})
data_dict[code].update(metadata)
if query_isodate:
data_dict[code]['last_refresh'] = query_isodate
return data_dict
def parse_site_infos(content_io, namespace, site_info_names):
"""parses information contained in site info elements out of a waterml file;
content_io should be a file-like object
"""
site_infos = {}
for site_info_name in site_info_names:
content_io.seek(0)
site_info_elements = [
element
for (event, element) in etree.iterparse(content_io)
if element.tag == namespace + site_info_name
]
site_info_dicts = [
_parse_site_info(site_info_element, namespace)
for site_info_element in site_info_elements
]
site_infos.update(dict([(d['code'], d) for d in site_info_dicts]))
return site_infos
def parse_sites(content_io, namespace):
"""parses information contained in site elements (including seriesCatalogs)
out of a waterml file; content_io should be a file-like object
"""
content_io.seek(0)
site_elements = [
ele for (event, ele) in etree.iterparse(content_io)
if ele.tag == namespace + 'site']
site_dicts = [
_parse_site(site_element, namespace)
for site_element in site_elements]
sites = dict(
[(site_dict['code'], site_dict)
for site_dict in site_dicts])
return sites
def parse_variables(content_io, namespace):
"""parses information contained in variables elements out of a waterml file;
content_io should be a file-like object
"""
content_io.seek(0)
variable_elements = [
element
for (event, element) in etree.iterparse(content_io)
if element.tag == namespace + 'variable'
]
variable_dicts = [
_parse_variable(variable_element, namespace)
for variable_element in variable_elements
]
variables = dict([
(variable_dict['code'], variable_dict)
for variable_dict in variable_dicts
])
return variables
def _element_dict(element, exclude_children=None, prepend_attributes=True):
"""converts an element to a dict representation with CamelCase tag names and
attributes converted to underscores; this is a generic converter for cases
where special parsing isn't necessary. In most cases you will want to
update with this dict. If prepend_element_name is True (default), then
attributes and children will be prepended with the parent element's tag
name.
Note: does not handle sibling elements
"""
if element is None:
return {}
if exclude_children is None:
exclude_children = []
element_dict = {}
element_name = util.camel_to_underscore(element.tag.split('}')[-1])
if len(element) == 0 and not element.text is None:
element_dict[element_name] = element.text
element_dict.update(dict([
(_element_dict_attribute_name(key, element_name,
prepend_element_name=prepend_attributes), value)
for key, value in element.attrib.items()
if value.split(':')[0] not in ['xsd', 'xsi']
]))
for child in element.iterchildren():
if not child.tag.split('}')[-1] in exclude_children:
element_dict.update(_element_dict(child))
return element_dict
def _element_dict_attribute_name(attribute_name, element_name,
prepend_element_name=True):
attribute_only = util.camel_to_underscore(attribute_name.split('}')[-1])
if attribute_only.startswith(element_name) or not prepend_element_name:
return attribute_only
else:
return element_name + '_' + attribute_only
def _find_unit(element, namespace):
unit_element = element.find(namespace + 'unit')
if unit_element is None:
unit_element = element.find(namespace + 'units')
return unit_element
def _parse_datetime(datetime_str):
"""returns an iso 8601 datetime string; USGS returns fractions of a second
which are usually all 0s. ISO 8601 does not limit the number of decimal
places but we have to cut them off at some point
"""
#XXX: this could be sped up if need be
#XXX: also, we need to document that we are throwing away fractions of
# seconds
return isodate.datetime_isoformat(isodate.parse_datetime(datetime_str))
def _parse_geog_location(geog_location, namespace):
"""returns a dict representation of a geogLocation etree element"""
return_dict = {
'latitude': geog_location.find(namespace + 'latitude').text,
'longitude': geog_location.find(namespace + 'longitude').text,
}
srs = geog_location.attrib.get('srs')
if not srs is None:
return_dict['srs'] = srs
return return_dict
def _parse_metadata(values_element, metadata_elements, namespace):
metadata = {}
for tag, collection_name, key in metadata_elements:
underscored_tag = util.camel_to_underscore(tag)
collection = [
_scrub_prefix(_element_dict(element, namespace),
underscored_tag)
for element in values_element.findall(namespace + tag)
]
if len([x for x in collection if len(x)]):
collection_dict = dict([
(item[key], item)
for item in collection
if key in item
])
metadata[collection_name] = collection_dict
return metadata
def _parse_method(method, namespace):
return _element_dict(method, namespace, prepend_attributes=False)
def _parse_series(series, namespace):
include_elements = [
'method',
'Method',
'source',
'Source',
'QualityControlLevel',
'qualityControlLevel',
'variableTimeInterval',
'valueCount',
]
series_dict = {}
variable_element = series.find(namespace + 'variable')
series_dict['variable'] = _parse_variable(variable_element, namespace)
for include_element in include_elements:
element = series.find(namespace + include_element)
if not element is None:
name = util.camel_to_underscore(element.tag)
element_dict = _scrub_prefix(_element_dict(element), name)
series_dict[name] = element_dict
return series_dict
def _parse_site(site, namespace):
"""returns a dict representation of a site given an etree object
representing a site element
"""
site_dict = _parse_site_info(site.find(namespace + 'siteInfo'), namespace)
series_elements = site.iter(namespace + 'series')
site_dict['series'] = [
_parse_series(series_element, namespace)
for series_element in series_elements
]
return site_dict
def _parse_site_info(site_info, namespace):
"""returns a dict representation of a site given an etree object
representing a siteInfo element
"""
site_code = site_info.find(namespace + "siteCode")
return_dict = {
'code': site_code.text,
'name': site_info.find(namespace + "siteName").text,
'network': site_code.attrib.get('network'),
}
agency = site_code.attrib.get('agencyCode')
if agency:
return_dict['agency'] = agency
geog_location = site_info.find(
namespace.join(["", "geoLocation/", "geogLocation"]))
if not geog_location is None:
return_dict['location'] = _parse_geog_location(geog_location, namespace)
timezone_info = site_info.find(namespace + "timeZoneInfo")
if not timezone_info is None:
return_dict['timezone_info'] = _parse_timezone_info(timezone_info, namespace)
elevation_m = site_info.find(namespace + 'elevation_m')
if not elevation_m is None:
return_dict['elevation_m'] = elevation_m.text
# WaterML 1.0 notes
notes = dict([
(util.camel_to_underscore(note.attrib['title'].replace(' ', '')),
note.text)
for note in site_info.findall(namespace + 'note')
])
if notes:
return_dict['notes'] = notes
# WaterML 1.1 siteProperties
site_properties = dict([
(util.camel_to_underscore(
site_property.attrib['name'].replace(' ', '')),
site_property.text)
for site_property in site_info.findall(namespace + 'siteProperty')
])
if site_properties:
return_dict['site_property'] = site_properties
return return_dict
def _parse_timezone_element(timezone_element):
"""returns a dict representation of a timezone etree element (either
defaultTimeZone or daylightSavingsTimeZone)
"""
return {
'abbreviation': timezone_element.attrib.get('zoneAbbreviation'),
'offset': timezone_element.attrib.get('zoneOffset'),
}
def _parse_timezone_info(timezone_info, namespace):
"""returns a dict representation of a timeZoneInfo etree element"""
return_dict = {}
uses_dst_str = timezone_info.attrib.get('siteUsesDaylightSavingsTime', "false")
if uses_dst_str == "true":
return_dict['uses_dst'] = True
else:
return_dict['uses_dst'] = False
dst_element = timezone_info.find(namespace + 'daylightSavingsTimeZone')
if not dst_element is None:
return_dict['dst_tz'] = _parse_timezone_element(dst_element)
return_dict['default_tz'] = _parse_timezone_element(
timezone_info.find(namespace + 'defaultTimeZone'))
return return_dict
def _parse_time_info(time_info_element, namespace):
"""returns a dict that represents a parsed WOF 1.0 timeSupport or WOF 1.1
timeScale element
"""
return_dict = {}
is_regular = time_info_element.attrib.get('isRegular')
if not is_regular is None:
if is_regular.lower() == 'true':
is_regular = True
elif is_regular.lower() == 'false':
is_regular = False
return_dict['is_regular'] = is_regular
if '1.0' in namespace:
interval_tag = 'timeInterval'
elif '1.1' in namespace:
interval_tag = 'timeSupport'
interval_element = time_info_element.find(namespace + interval_tag)
if not interval_element is None:
return_dict['interval'] = interval_element.text
unit_element = _find_unit(time_info_element, namespace)
if not unit_element is None:
return_dict['units'] = _parse_unit(unit_element, namespace)
return return_dict
def _parse_unit(unit_element, namespace):
"""returns a list of dicts that represent the values for a given unit or
units element
"""
unit_dict = _element_dict(unit_element)
tag_name = unit_element.tag.split('}')[-1]
return_dict = {}
if '1.0' in namespace:
return_dict['name'] = unit_element.text
keys = [
'abbreviation',
'code',
'name',
'type',
]
for key in keys:
dict_key = tag_name + '_' + key
if dict_key in unit_dict:
return_dict[key] = unit_dict[dict_key]
return return_dict
def _parse_value(value_element, namespace):
value_dict = _element_dict(value_element, prepend_attributes=False)
datetime = _parse_datetime(value_dict.pop('date_time'))
value_dict['datetime'] = datetime
return value_dict
def _parse_values(values_element, namespace):
"""returns a list of dicts that represent the values for a given etree
values element
"""
return [
_parse_value(value, namespace)
for value in values_element.findall(namespace + 'value')
]
def _parse_variable(variable_element, namespace):
"""returns a dict that represents a variable for a given etree variable element"""
return_dict = _element_dict(variable_element,
exclude_children=['options', 'timeScale', 'timeSupport', 'unit', 'units',
'variableCode', 'variableDescription', 'variableName'])
variable_code = variable_element.find(namespace + 'variableCode')
return_dict.update({
'code': variable_code.text,
'id': variable_code.attrib.get('variableID'),
'name': variable_element.find(namespace + 'variableName').text,
'vocabulary': variable_code.attrib.get('vocabulary'),
})
network = variable_code.attrib.get('network')
if network:
return_dict['network'] = network
statistic = variable_element.find(namespace + 'options/' + namespace + "option[@name='Statistic']")
if statistic is not None:
return_dict['statistic'] = {
'code': statistic.attrib.get('optionCode'),
'name': statistic.text,
}
if '1.0' in namespace:
time_info_name = 'timeSupport'
elif '1.1' in namespace:
time_info_name = 'timeScale'
time_info_element = variable_element.find(namespace + time_info_name)
if not time_info_element is None:
return_dict['time'] = _parse_time_info(time_info_element, namespace)
unit_element = _find_unit(variable_element, namespace)
if not unit_element is None:
return_dict['units'] = _parse_unit(unit_element, namespace)
variable_description = variable_element.find(
namespace + 'variableDescription')
if not variable_description is None:
return_dict['description'] = variable_description.text
return return_dict
def _scrub_prefix(element_dict, prefix):
"returns a dict with prefix scrubbed from the keys"
return dict([
(k.split(prefix + '_')[-1], v)
for k, v in element_dict.items()
])
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