wps_climdexInput_quantile

WPS wrapper for climdexInput.quantile, which is a reimplementation of R’s type=8 created to improve the efficiency of this package.

import os
import requests
from birdy import WPSClient
from rpy2 import robjects
from urllib.request import urlretrieve
from importlib.resources import files
from tempfile import NamedTemporaryFile

from wps_tools.R import construct_r_out, test_rda_output
from wps_tools.testing import get_target_url

# Ensure we are in the working directory with access to the data
while os.path.basename(os.getcwd()) != "quail":
    os.chdir('../')

# NBVAL_IGNORE_OUTPUT
url = get_target_url("quail")
print(f"Using quail on {url}")

Using quail on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/quail/wps

quail = WPSClient(url)

Help for individual processes can be diplayed using the ? command (ex/ bird.process?)

# NBVAL_IGNORE_OUTPUT
quail.climdex_quantile?

Signature:
quail.climdex_quantile(
    quantiles_vector,
    data_vector='data_vector',
    loglevel='INFO',
    data_file=None,
    output_file='output.rda',
    vector_name='days',
    output_formats=None,
)
Docstring:
Implements R’s type=8 in a more efficient manner

Parameters
----------
data_file : ComplexData:mimetype:`application/x-gzip`
    Path to the file containing data to compute quantiles on.
data_vector : string
    R double vector data to compute quantiles on. Only neeed when data_rds is used.
quantiles_vector : string
    Quantiles to be computed
output_file : string
    Filename to store the output Rdata (extension .rda)
vector_name : string
    Name to label the output vector
loglevel : {'CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET'}string
    Logging level

Returns
-------
output_vector : string
    A vector of the quantiles in question
rda_output : ComplexData:mimetype:`application/x-gzip`
    Rda file containing R output data
File:      ~/github/quail/</tmp/quail-venv/lib/python3.8/site-packages/birdy/client/base.py-11>
Type:      method

Run wps_climdex_quantile process

Run with data extracted from a file

with NamedTemporaryFile(suffix=".rda", prefix="quantile_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_quantile(
            data_file=(files("tests") / "data/ec.1018935.rda").resolve(),
            data_vector="unlist(ec.1018935.tmax['MAX_TEMP'])",
            quantiles_vector="c(0.1, 0.5, 0.9)",
            vector_name="tmax_quantiles",
        )
quantile_url = output.get()[1]

test_rda_output(
    quantile_url, "tmax_quantiles", "expected_quantiles.rda", "expected_tmax_quantiles"
    )

Run with manually created data

with NamedTemporaryFile(suffix=".rda", prefix="quantile_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_quantile(
            data_vector="0:10",
            quantiles_vector="0.5",
            vector_name="quantile_50p",
        )
quantile_data = output.get()[0]

assert quantile_data.split()[1] == "5"

You can also use rds input

with NamedTemporaryFile(suffix=".rda", prefix="quantile_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_quantile(
            data_file=(files("tests") / "data/ec.1018935.MAX_TEMP.rds").resolve(),
            quantiles_vector="c(0.1, 0.5, 0.9)",
            vector_name="tmax_quantiles",
        )
quantile_url = output.get()[1]

You can access your output with construct_r_out from wps_tools.R

# NBVAL_IGNORE_OUTPUT
construct_r_out(output.get())[0]

[R object with classes: ('numeric',) mapped to:
 [7.000000, 12.800000, 21.100000]]