def _get_all_granule_pages(session, url, entry_map, max_paging_depth=1000000):
"""Helper function for searching through all pages for a collection.
Parameters
-----------
session: :class:`requets.Session`, optional
An authenticated Earthdata login session
url: str
URL to website
entry_map: function
Function for mapping the entries to a desired format
max_paging_depth
"""
page_size = int([
q for q in url.split("?")[1].split("&") if "page_size" in q
][0].split("=")[1])
max_pages = int(max_paging_depth / page_size)
pydict = _get_from_url(url, session).json()
entries = list(map(entry_map, pydict["feed"]["entry"]))
for i in range(1, max_pages):
page_url = url + "&page_num=%d" % (i + 1)
page_entries = _get_from_url(page_url, session).json()["feed"]["entry"]
if not page_entries:
break
entries.extend(list(map(entry_map, page_entries)))
return entries
def from_url(cls, url):
"""
Create podpac Node from a WMS/WCS request.
Arguments
---------
url : str, dict
The raw WMS/WCS request url, or a dictionary of query parameters
Returns
-------
:class:`Node`
A full Node with sub-nodes based on the definition of the node from the URL
Notes
-------
The request can specify the PODPAC node by four different mechanism:
* Direct node name: PODPAC will look for an appropriate node in podpac.datalib
* JSON definition passed using the 'PARAMS' query string: Need to specify the special LAYER/COVERAGE value of
"%PARAMS%"
* By pointing at the JSON definition retrievable with a http GET request:
e.g. by setting LAYER/COVERAGE value to https://my-site.org/pipeline_definition.json
* By pointing at the JSON definition retrievable from an S3 bucket that the user has access to:
e.g by setting LAYER/COVERAGE value to s3://my-bucket-name/pipeline_definition.json
"""
params = _get_query_params_from_url(url)
if _get_param(params, "SERVICE") == "WMS":
layer = _get_param(params, "LAYERS")
elif _get_param(params, "SERVICE") == "WCS":
layer = _get_param(params, "COVERAGE")
d = None
if layer.startswith("https://"):
d = _get_from_url(layer).json()
elif layer.startswith("s3://"):
parts = layer.split("/")
bucket = parts[2]
key = "/".join(parts[3:])
s3 = S3CacheStore(s3_bucket=bucket)
s = s3._load(key)
elif layer == "%PARAMS%":
s = _get_param(params, "PARAMS")
else:
p = _get_param(params, "PARAMS")
if p is None:
p = "{}"
d = OrderedDict({
layer.replace(".", "-"): {
"node": layer,
"attrs": json.loads(p)
}
})
if d is None:
d = json.loads(s, object_pairs_hook=OrderedDict)
return cls.from_definition(d)
def calibration_data(self):
cd = _get_from_url(self.station_calibration_url)
if cd is None:
raise ConnectionError(
"COSMOS data cannot be retrieved. Is the site {} down?".format(
self.station_calibration_url))
cd = cd.json()
cd["items"] = [_convert_str_to_vals(i) for i in cd["items"]]
return cd
def _property_source_default(self):
v = _infer_SMAP_product_version("SPL4SMLM", SMAP_BASE_URL(),
self.session)
url = SMAP_BASE_URL() + "/SPL4SMLM.%03d/2015.03.31/" % (v)
r = _get_from_url(url, session=self.session)
if not r:
return "None"
n = self.file_url_re.search(r.text).group()
return url + n
def search_granule_json(session=None, entry_map=None, **kwargs):
"""Search for specific files from NASA CMR for a particular collection
Parameters
-----------
session: :class:`requets.Session`, optional
An authenticated Earthdata login session
entry_map: function
A function applied to each individual entry. Could be used to filter out certain data in an entry
**kwargs: dict
Additional query string parameters.
At minimum the provider, provider_id, concept_id, collection_concept_id, short_name, version, or entry_title
need to be provided for a granule search.
Returns
---------
list
Entries for each granule in the collection based on the search terms
"""
base_url = CMR_URL + "granules.json?"
if not np.any([
m not in kwargs for m in [
"provider",
"provider_id",
"concept_id",
"collection_concept_id",
"short_name",
"version",
"entry_title",
]
]):
raise ValueError(
"Need to provide either"
" provider, provider_id, concept_id, collection_concept_id, short_name, version or entry_title"
" for granule search.")
if "page_size" not in kwargs:
kwargs["page_size"] = "2000"
if entry_map is None:
entry_map = lambda x: x
query_string = "&".join([k + "=" + str(v) for k, v in kwargs.items()])
if session is None:
session = requests
url = base_url + query_string
if "page_num" not in kwargs:
entries = _get_all_granule_pages(session, url, entry_map)
else:
pydict = _get_from_url(url, session).json()
entries = list(map(entry_map, pydict["feed"]["entry"]))
return entries
def raw_data(self):
_logger.info("Downloading station data from {}".format(
self.station_data_url))
r = _get_from_url(self.station_data_url)
if r is None:
raise ConnectionError(
"COSMOS data cannot be retrieved. Is the site {} down?".format(
self.station_calibration_url))
return r.text
def _stations_data_raw(self):
url = self.url + self.stations_url
r = _get_from_url(url)
t = r.text
# Fix the JSON
t_f = re.sub(':\s?",', ': "",', t) # Missing closing parenthesis
if t_f[-5:] == ",\n]}\n": # errant comma
t_f = t_f[:-5] + "\n]}\n"
return t_f
def site_properties(self):
r = _get_from_url(self.station_properties_url)
soup = bs4.BeautifulSoup(r.text, "lxml")
regex = re.compile("Soil Organic Carbon")
loc = soup.body.findAll(text=regex)[0].parent.parent
label, value = loc.findAll("div")
labels = [l.strip() for l in label.children if "br" not in str(l)]
values = [l.strip() for l in value.children if "br" not in str(l) and l.strip() != ""]
properties = {k: v for k, v in zip(labels, values)}
return _convert_str_to_vals(properties)
def _stations_data_raw(self):
url = self.url + self.stations_url
r = _get_from_url(url)
if r is None:
raise ConnectionError(
"COSMOS data cannot be retrieved. Is the site {} down?".format(
url))
t = r.text
# Fix the JSON
t_f = re.sub(':\s?",', ': "",', t) # Missing closing parenthesis
if t_f[-5:] == ",\n]}\n": # errant comma
t_f = t_f[:-5] + "\n]}\n"
return t_f
def get_collection_entries(session=None,
short_name=None,
keyword=None,
**kwargs):
"""Uses NASA CMR to retrieve metadata about a collection
Parameters
-----------
session: :class:`requets.Session`, optional
An authenticated Earthdata login session
short_name: str, optional
The short name of the dataset
keyword: str, optional
Any keyword search parameters
**kwargs: str, optional
Any additional query parameters
Returns
---------
list:
A list of collection metadata dictionaries
Examples:
-----------
>>> # This make the following request https://cmr.earthdata.nasa.gov/search/collections.json?short_name=SPL2SMAP_S
>>> get_collection_id(short_name='SPL2SMAP_S')
['C1522341104-NSIDC_ECS']
"""
base_url = CMR_URL + "collections.json?"
if short_name is not None:
kwargs["short_name"] = short_name
if keyword is not None:
kwargs["keyword"] = keyword
query_string = "&".join([k + "=" + v for k, v in kwargs.items()])
# use generic requests session if `session` is not defined
if session is None:
session = requests
pydict = _get_from_url(base_url + query_string, session).json()
entries = pydict["feed"]["entry"]
return entries
def available_dates(self):
""" Available dates in SMAP date format, sorted."""
url = "/".join(
[self.base_url,
"%s.%03d" % (self.product, self.version)])
r = _get_from_url(url, self.session)
if r is None:
_logger.warning(
"Could not contact {} to retrieve source coordinates".format(
url))
return []
soup = BeautifulSoup(r.text, "lxml")
matches = [
self.date_url_re.match(a.get_text()) for a in soup.find_all("a")
]
dates = [m.group() for m in matches if m]
return dates
def site_properties(self):
r = _get_from_url(self.station_properties_url)
if r is None:
raise ConnectionError(
"COSMOS data cannot be retrieved. Is the site {} down?".format(
self.station_properties_url))
soup = bs4.BeautifulSoup(r.text, "lxml")
regex = re.compile("Soil Organic Carbon")
loc = soup.body.findAll(text=regex)[0].parent.parent
label, value = loc.findAll("div")
labels = [l.strip() for l in label.children if "br" not in str(l)]
values = [
l.strip() for l in value.children
if "br" not in str(l) and l.strip() != ""
]
properties = {k: v for k, v in zip(labels, values)}
return _convert_str_to_vals(properties)
def _infer_SMAP_product_version(product, base_url, session):
"""Helper function to automatically infer the version number of SMAP
products in case user did not specify a version, or the version changed
Parameters
------------
product: str
Name of the SMAP product (e.g. one of SMAP_PRODUCT_DICT.keys())
base_url: str
URL to base SMAP product page
session: :class:`requests.Session`
Authenticated EDS session. Generally returned from :class:`SMAPSessionMixin`.
"""
r = _get_from_url(base_url, session=session)
if r:
m = re.search(product, r.text)
return int(r.text[m.end() + 1:m.end() + 4])
return int(
SMAP_PRODUCT_MAP.sel(product=product, attr="default_version").item())
def available_coords_sources(self):
"""Read NSIDC site for available coordinate sources
Returns
-------
np.ndarray
Available times of sources in the folder
np.ndarray
Available lat lon coordinates of sources in the folder, None if empty
np.ndarray
The url's of the sources
Raises
------
RuntimeError
If the NSIDC website cannot be accessed
"""
r = _get_from_url(self.folder_url, self.session)
if r is None:
_logger.warning(
"Could not contact {} to retrieve source coordinates".format(
self.folder_url))
return np.array([]), None, np.array([])
soup = BeautifulSoup(r.text, "lxml")
a = soup.find_all("a")
file_regex = self.file_url_re
file_regex2 = self.file_url_re2
date_time_regex = self.date_time_url_re
date_regex = self.date_url_re
latlon_regex = self.latlon_url_re
times = []
latlons = []
sources = []
for aa in a:
t = aa.get_text().strip("\n")
if "h5.iso.xml" in t:
continue
m = file_regex.match(t)
m2 = file_regex2.match(t)
lonlat = None
if m:
date_time = date_time_regex.search(m.group()).group()
times.append(smap2np_date(date_time))
elif m2:
m = m2
date = date_regex.search(m.group()).group()
times.append(smap2np_date(date))
if m:
sources.append(m.group())
lonlat = latlon_regex.search(m.group())
if lonlat:
lonlat = lonlat.group()
latlons.append((
float(lonlat[4:6]) * (1 - 2 * (lonlat[6] == "S")),
float(lonlat[:3]) * (1 - 2 * (lonlat[3] == "W")),
))
times = np.atleast_1d(np.array(times).squeeze())
latlons = np.array(latlons)
sources = np.array(sources)
I = np.argsort(times)
if latlons.shape[0] == times.size:
return times[I], latlons[I], sources[I]
return times[I], None, sources[I]
def calibration_data(self):
cd = _get_from_url(self.station_calibration_url).json()
cd["items"] = [_convert_str_to_vals(i) for i in cd["items"]]
return cd
