Test to see if we can SEARCH, ACCESS and USE data using IOOS supported service protocols.
SEARCH a CSW Endpoint to find all datasets that: are containing within a specific bounding box have a specified variable of interest fall withing a specified date range contain a specific data access service type
ACCESS data from the discovered data endpoints
USE the data and see if we can use the data (to the extent of making a time series plot with a labeled x-axis).
In [1]:
from pylab import *
from owslib.csw import CatalogueServiceWeb
from owslib import fes
import random
import netCDF4
import pandas as pd
import datetime as dt
These are tags NGDC would like tested:
apiso:ResponsiblePartyName
apiso:Keywords
apiso:KeywordType
apiso:VertExtent_min
apiso:VertExtent_max
apiso:ServiceType
apiso:ServiceTypeVersion
apiso:OperatesOn
resource.url
website.url
In [2]:
#from IPython.core.display import HTML
#HTML('<iframe src=http://www.ngdc.noaa.gov/geoportal/ width=950 height=400></iframe>')
In [3]:
# connect to CSW, explore it's properties
endpoint = 'http://www.ngdc.noaa.gov/geoportal/csw' # NGDC Geoportal
#endpoint = 'http://www.nodc.noaa.gov/geoportal/csw' # NODC Geoportal: granule level
#endpoint = 'http://data.nodc.noaa.gov/geoportal/csw' # NODC Geoportal: collection level
#endpoint = 'http://geodiscover.cgdi.ca/wes/serviceManagerCSW/csw' # NRCAN CUSTOM
#endpoint = 'http://geoport.whoi.edu/gi-cat/services/cswiso' # USGS Woods Hole GI_CAT
#endpoint = 'http://cida.usgs.gov/gdp/geonetwork/srv/en/csw' # USGS CIDA Geonetwork
#endpoint = 'http://cmgds.marine.usgs.gov/geonetwork/srv/en/csw' # USGS Coastal and Marine Program
#endpoint = 'http://geoport.whoi.edu/geoportal/csw' # USGS Woods Hole Geoportal
#endpoint = 'http://geo.gov.ckan.org/csw' # CKAN testing site for new Data.gov
#endpoint = 'https://edg.epa.gov/metadata/csw' # EPA
#endpoint = 'http://cwic.csiss.gmu.edu/cwicv1/discovery' # CWIC
csw = CatalogueServiceWeb(endpoint,timeout=60)
csw.version
Out[3]:
In [4]:
[op.name for op in csw.operations]
Out[4]:
In [5]:
# hopefully something like this will be implemented in fes soon
def dateRange(start_date='1900-01-01',stop_date='2100-01-01',constraint='overlaps'):
if constraint == 'overlaps':
start = fes.PropertyIsLessThanOrEqualTo(propertyname='apiso:TempExtent_begin', literal=stop_date)
stop = fes.PropertyIsGreaterThanOrEqualTo(propertyname='apiso:TempExtent_end', literal=start_date)
elif constraint == 'within':
start = fes.PropertyIsGreaterThanOrEqualTo(propertyname='apiso:TempExtent_begin', literal=start_date)
stop = fes.PropertyIsLessThanOrEqualTo(propertyname='apiso:TempExtent_end', literal=stop_date)
return start,stop
In [6]:
# hopefully something like this will be implemented in fes soon
def zRange(min_z='-5000', max_z='0', constraint='overlaps'):
if constraint == 'overlaps':
zmin = fes.PropertyIsLessThanOrEqualTo(propertyname='apiso:VertExtent_min', literal=min_z)
zmax = fes.PropertyIsGreaterThanOrEqualTo(propertyname='apiso:VertExtent_max', literal=max_z)
elif constraint == 'within':
zmin = fes.PropertyIsGreaterThanOrEqualTo(propertyname='apiso:VertExtent_min', literal=min_z)
zmax = fes.PropertyIsLessThanOrEqualTo(propertyname='apiso:VertExtent_max', literal=max_z)
return zmin,zmax
In [7]:
# User Input for query
#box=[-120, 2.0, -110.0, 6.0] # oceansites
box=[-160, 19, -156, 23] # pacioos
start_date='2012-05-01'
stop_date='2012-06-01'
min_z = '-5000'
max_z = '0'
responsible_party = 'Margaret McManus'
std_name = 'sea_water_temperature'
service_type='opendap'
In [8]:
# convert User Input into FES filters
start,stop = dateRange(start_date,stop_date)
zmin,zmax = zRange(min_z,max_z,constraint='within')
bbox = fes.BBox(box)
#keywords = fes.PropertyIsLike(propertyname='anyText', literal=std_name)
#keywords = fes.PropertyIsLike(propertyname='apiso:Keywords', literal=std_name)
keywords = fes.PropertyIsEqualTo(propertyname='apiso:Keywords', literal=std_name)
serviceType = fes.PropertyIsLike(propertyname='apiso:ServiceType', literal=('*%s*' % service_type))
ResponsiblePartyName = fes.PropertyIsEqualTo(propertyname='apiso:ResponsiblePartyName', literal=responsible_party)
#serviceType = fes.PropertyIsEqualTo(propertyname='apiso:ServiceType', literal=service_type)
In [9]:
# try simple request using only keywords
csw.getrecords2(constraints=[keywords],maxrecords=5)
csw.records.keys()
Out[9]:
In [10]:
# try request using multiple filters "and" syntax: [[filter1,filter2]]
csw.getrecords2(constraints=[[keywords,start,stop,serviceType,bbox]],maxrecords=5,esn='full')
csw.records.keys()
Out[10]:
In [11]:
# try request using multiple filters "and" syntax: [[filter1,filter2]]
csw.getrecords2(constraints=[[keywords,start,stop,bbox]],maxrecords=5,esn='full')
csw.records.keys()
Out[11]:
In the next cell we take a look at the references for a random record. The ServiceType for the OPeNDAP Data URL below is ServiceType:odp:url, which seems correct!
In [12]:
choice=random.choice(list(csw.records.keys()))
print choice
csw.records[choice].references
Out[12]:
In the next cell we try using the ResponsiblePartyName, we are looking for Margaret McMannus, who we see in the ISO record for NS10agg here
http://oos.soest.hawaii.edu/thredds/iso/hioos/nss/ns10agg?catalog=http%3A%2F%2Foos.soest.hawaii.edu%2Fthredds%2Fidd%2Fnss_hioos.html&dataset=NS10agg
In [13]:
# try adding responsible party role
csw.getrecords2(constraints=[ResponsiblePartyName],maxrecords=10,esn='full')
csw.records.keys()
Out[13]:
Now print out some titles
In [14]:
for rec,item in csw.records.iteritems():
print item.title
In the next cell we try using a vertical extent range, which doesn't seem to be working, as we are looking for z values between [-5000, 0] and we see in the ISO record for 'NS10agg' here:
http://oos.soest.hawaii.edu/thredds/iso/hioos/nss/ns10agg?catalog=http%3A%2F%2Foos.soest.hawaii.edu%2Fthredds%2Fidd%2Fnss_hioos.html&dataset=NS10agg
that the vertical extent is from [-2, -2]
In [15]:
csw.getrecords2(constraints=[[keywords,start,stop,serviceType,bbox,zmin,zmax]],maxrecords=5,esn='full')
csw.records.keys()
Out[15]:
Define a function that will return the endpoint for a specified service type
In [16]:
# get specific ServiceType URL from records
def service_urls(records,service_string='urn:x-esri:specification:ServiceType:odp:url'):
urls=[]
for key,rec in records.iteritems():
#create a generator object, and iterate through it until the match is found
#if not found, gets the default value (here "none")
url = next((d['url'] for d in rec.references if d['scheme'] == service_string), None)
if url is not None:
urls.append(url)
return urls
Print out all the OPeNDAP Data URL endpoints
In [17]:
dap_urls = service_urls(csw.records,service_string='urn:x-esri:specification:ServiceType:odp:url')
print "\n".join(dap_urls)
In [18]:
from collections import defaultdict
def standard_names(ncv):
'''
get dictionary of variables with standard_names
'''
d = defaultdict(list)
for k,v in ncv.iteritems():
if 'standard_name' in v.ncattrs():
d[v.standard_name].append(k)
return d
In [19]:
for url in dap_urls:
ncv = netCDF4.Dataset(url).variables
lat = ncv['lon'][:]
lon = ncv['lat'][:]
tvar = ncv['time']
istart = netCDF4.date2index(dt.datetime.strptime(start_date,'%Y-%m-%d'),tvar,select='nearest')
istop = netCDF4.date2index(dt.datetime.strptime(stop_date,'%Y-%m-%d'),tvar,select='nearest')
if istart != istop:
dtime = netCDF4.num2date(tvar[istart:istop],tvar.units)
# make a dictionary containing all data from variables that matched the standard_name
# find list of variables for each standard_name
d = standard_names(ncv)
# find all the variables matching standard_name=std_name
print d[std_name]
# read all the data into a dictionary
data_dict={}
lev=0
for v in d[std_name]:
data_dict[v]=ncv[v][istart:istop].flatten()
# Create Pandas data frame, with time index
ts = pd.DataFrame.from_dict(data_dict)
ts.index=dtime
ts.plot(figsize=(12,4));
title(std_name)
In []:
HTML(html)