Fix for Thredds v5 output update #101
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``` _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 0 _ Notebook cell execution failed Cell 0: Cell outputs differ Input: from siphon.catalog import TDSCatalog url = "https://boreas.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip6/ouranos/ESPO-G/ESPO-G6-R2v1.0.0/catalog.xml" # TEST_USE_PROD_DATA # Create Catalog cat = TDSCatalog(url) # List of datasets print(f"Number of datasets: {len(cat.datasets)}") # Access mechanisms - here we are interested in OPENDAP, a data streaming protocol cds = cat.datasets[0] print(f"Access URLs: {tuple(cds.access_urls.keys())}") Traceback: mismatch 'stdout' assert reference_output == test_output failed: "Number of da...cdfSubset')\n" == "Number of da...cdfSubset')\n" Skipping 43 identical leading characters in diff, use -v to show Skipping 50 identical trailing characters in diff, use -v to show - erver', 'OpenDAP', 'NC ? ^^^ + erver', 'OPENDAP', 'NC ? ^^^ _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 2 _ Notebook cell execution failed Cell 2: Cell outputs differ Input: # Extract a subset of the file # Again, this only creates an in-memory representation of the data sub = ds.tasmin.sel(time="2050").isel(rlon=400, rlat=350) # The data is only downloaded when we actually need it for a computation. sub.mean(keep_attrs=True).compute() Traceback: mismatch 'text/plain' assert reference_output == test_output failed: '<xarray.Data...60 50 50]' == '<xarray.Data...60 50 50]' Skipping 38 identical leading characters in diff, use -v to show Skipping 225 identical trailing characters in diff, use -v to show B - array(279.47516, dtype=float32) ? ^ - ^^ + array(278.72336, dtype=float32) ? ^ ^^^ Coordinates: rlat float32 4B -14.67 rlon float32 4B 360.6 rotated_pole float32 4B 9.969e+36 lat float32 4B 43.57 lon float32 4B -91.6 Attributes: - long_name: Minimal daily temperature cell_methods: time: minimum within days description: Daily minimal temperature as... grid_mapping: rotated_pole history: [DATE_TIME] Data c... + long_name: Minimal daily temperature stan _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 3 _ Notebook cell execution failed Cell 3: Cell outputs differ Input: ssp245_data = [cat.datasets[x] for x in cat.datasets if "ssp245" in x] ssp245_data Traceback: mismatch 'text/plain' assert reference_output == test_output failed: '[day_ESPO-G6...1001231.ncml]' == '[day_ESPO-G6...1001231.ncml]' Skipping 35 identical leading characters in diff, use -v to show - ioMIP_NAM_AS-RCEC_TaiESM1_ssp245_r1i1p1f1_19500101-21001231.ncml, ? ^ ^^^^^ ^^^ ^ + ioMIP_NAM_NUIST_NESM3_ssp245_r1i1p1f1_19500101-21001231.ncml, ? ^^^ ^ ^ ^ + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NOAA-GFDL_GFDL-ESM4_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NIMS-KMA_KACE-1-0-G_ssp245_r1i1p1f1_19500101-21001230.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-MM_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-LM_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MRI_MRI-ESM2-0_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-HR_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MOHC_UKESM1-0-LL_ssp245_r1i1p1f2_19500101-21001230.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC6_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC-ES2L_ssp245_r1i1p1f2_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_IPSL_IPSL-CM6A-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM5-0_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM4-8_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3-Veg_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3-CC_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO_ACCESS-ESM1-5_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO-ARCCSS_ACCESS-CM2_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-ESM2-1_ssp245_r1i1p1f2_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-CM6-1_ssp245_r1i1p1f2_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CMCC_CMCC-ESM2_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CCCma_CanESM5_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CAS_FGOALS-g3_ssp245_r1i1p1f1_19500101-21001231.ncml, day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_BCC_BCC-CSM2-MR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CAS_FGOALS-g3_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CCCma_CanESM5_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CMCC_CMCC-ESM2_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-CM6-1_ssp245_r1i1p1f2_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-ESM2-1_ssp245_r1i1p1f2_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO-ARCCSS_ACCESS-CM2_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO_ACCESS-ESM1-5_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3-CC_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3-Veg_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_EC-Earth-Consortium_EC-Earth3_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM4-8_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM5-0_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_IPSL_IPSL-CM6A-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC-ES2L_ssp245_r1i1p1f2_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC6_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MOHC_UKESM1-0-LL_ssp245_r1i1p1f2_19500101-21001230.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-HR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MRI_MRI-ESM2-0_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-LM_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-MM_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NIMS-KMA_KACE-1-0-G_ssp245_r1i1p1f1_19500101-21001230.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NOAA-GFDL_GFDL-ESM4_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NUIST_NESM3_ssp245_r1i1p1f1_19500101-21001231.ncml] ? ^^^ ^^ ^ + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_AS-RCEC_TaiESM1_ssp245_r1i1p1f1_19500101-21001231.ncml] ? ^ ++++++ ^^ ^ _ PAVICS-landing-master/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-1DataAccess.ipynb::Cell 4 _ Notebook cell execution failed Cell 4: Cell outputs differ Input: tcr_likely_models = [ "BCC-CSM2-MR", "FGOALS-g3", "CMCC-ESM2", "CNRM-ESM2-1", "ACCESS-CM2", "ACCESS-ESM1-5", "MPI-ESM1-2-HR", "INM-CM5-0", "MIROC6", "MPI-ESM1-2-LR", "MRI-ESM2-0", "NorESM2-LM", "KACE-1-0-G", "GFDL-ESM4", "MIROC-ES2L", ] def _filter_tcr_likely(files): return [d for d in files if any([h in d.name for h in tcr_likely_models])] # create a simple search sub-function def get_ncfilelist(scen=None, url=None, tcr_likely=False): cat = TDSCatalog(url) ncfiles = [cat.datasets[c] for c in cat.datasets if scen in c] if tcr_likely: expected = len(tcr_likely_models) ncfiles = _filter_tcr_likely(ncfiles) if len(ncfiles) == expected: display(f"Successfully found {expected} datasets for {scen}") return ncfiles else: raise ValueError( f"Expected number of datasets for {scen} is {expected} : found {len(ncfiles)}" ) datasets = {} for scen in ["ssp245", "ssp370"]: datasets[scen] = get_ncfilelist(scen=scen, url=url, tcr_likely=True) display(datasets["ssp245"]) display(datasets["ssp370"]) Traceback: mismatch 'text/plain' assert reference_output == test_output failed: '[day_ESPO-G6...1001231.ncml]' == '[day_ESPO-G6...1001231.ncml]' Skipping 35 identical leading characters in diff, use -v to show - ioMIP_NAM_BCC_BCC-CSM2-MR_ssp245_r1i1p1f1_19500101-21001231.ncml, ? ^^^ ^^^ ^ ^^^^ + ioMIP_NAM_NOAA-GFDL_GFDL-ESM4_ssp245_r1i1p1f1_19500101-21001231.ncml, ? ^^^^^^^^^ ^^^^ ^ ^ + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NIMS-KMA_KACE-1-0-G_ssp245_r1i1p1f1_19500101-21001230.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-LM_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MRI_MRI-ESM2-0_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-HR_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC6_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC-ES2L_ssp245_r1i1p1f2_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM5-0_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO_ACCESS-ESM1-5_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO-ARCCSS_ACCESS-CM2_ssp245_r1i1p1f1_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-ESM2-1_ssp245_r1i1p1f2_19500101-21001231.ncml, + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CMCC_CMCC-ESM2_ssp245_r1i1p1f1_19500101-21001231.ncml, day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CAS_FGOALS-g3_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CMCC_CMCC-ESM2_ssp245_r1i1p1f1_19500101-21001231.ncml, ? ^^ ^^ ^ ^^ + day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_BCC_BCC-CSM2-MR_ssp245_r1i1p1f1_19500101-21001231.ncml] ? ^ ^ ^ +++ ^ - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CNRM-CERFACS_CNRM-ESM2-1_ssp245_r1i1p1f2_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO-ARCCSS_ACCESS-CM2_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_CSIRO_ACCESS-ESM1-5_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_INM_INM-CM5-0_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC-ES2L_ssp245_r1i1p1f2_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MIROC_MIROC6_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-HR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MPI-M_MPI-ESM1-2-LR_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_MRI_MRI-ESM2-0_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NCC_NorESM2-LM_ssp245_r1i1p1f1_19500101-21001231.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NIMS-KMA_KACE-1-0-G_ssp245_r1i1p1f1_19500101-21001230.ncml, - day_ESPO-G6-R2_v1.0.0_CMIP6_ScenarioMIP_NAM_NOAA-GFDL_GFDL-ESM4_ssp245_r1i1p1f1_19500101-21001231.ncml] ```
…output for Thredds v5
```
_ PAVICS-landing-fix-for-Thredds-v5-output-update/content/notebooks/climate_indicators/PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb::Cell 0 _
Notebook cell execution failed
Cell 0: Cell outputs differ
Input:
import os
os.environ["USE_PYGEOS"] = "0" # force use Shapely with GeoPandas
import warnings
import geopandas as gpd
import matplotlib.pyplot as plt
import numba
import xarray as xr
from clisops.core import subset
from dask.diagnostics import ProgressBar
from siphon.catalog import TDSCatalog
from xclim import atmos
warnings.simplefilter("ignore")
# TODO change address
url = "https://boreas.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/simulations/bias_adjusted/cmip6/ouranos/ESPO-G/ESPO-G6-R2v1.0.0/catalog.xml" # TEST_USE_PROD_DATA
# Create Catalog
cat = TDSCatalog(url)
# Subset over the Gasp�� peninsula in eastern Quebec
gaspe = gpd.GeoDataFrame.from_file(
"/notebook_dir/pavics-homepage/tutorial_data/gaspesie_mrc.geojson"
)
ds = subset.subset_shape(
xr.open_dataset(
cat.datasets[0].access_urls["OPENDAP"],
chunks=dict(time=365 * 4, rlon=50, rlat=50),
),
shape=gpd.GeoDataFrame(geometry=gaspe.buffer(0.05)),
)
# What we see here is only a representation of the full content, the entire data set hasn't been loaded.
display(ds)
# plot of single day tasmin
a = ds.tasmin.isel(time=0).plot(figsize=(10, 4))
Traceback:
mismatch 'text/plain'
assert reference_output == test_output failed:
'<xarray.Data... EPSG:4326' == '<xarray.Data... EPSG:4326'
Skipping 1172 identical leading characters in diff, use -v to show
- tes: (12/83)
? ^
+ tes: (12/81)
? ^
Conventions: CF-1.7 CMIP-6.2
Notes: Regridded on the grid of RDRS v2.1, then...
activity_id: CMIP
- branch_method: Hybrid-restart from year/DATE/of p...
- branch_time: 0.0
? -- ^^^^^
+ branch_method: standard
? ++++ ^^^^^^^^
branch_time_in_child: 0.0
+ branch_time_in_parent: 109573.0
... ...
license_type: permissive
terms_of_use: In addition to the provided licence, the...
attribution: Use of this dataset should be acknowledg...
modeling_realm: atmos
- source_institution: AS-RCEC
? ^ ^^^^^
+ source_institution: NUIST
? ^^^ ^
crs: EPSG:4326
```
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This was referenced Dec 5, 2024
tlvu
added a commit
to bird-house/birdhouse-deploy
that referenced
this pull request
Dec 5, 2024
## Overview Unidata has dropped support for TDS versions < 5.x. This updates Thredds to version 5.5. Requires matching update: * Ouranosinc/pavics-sdi#341 * Ouranosinc/pavics-sdi#342 * Ouranosinc/PAVICS-landing#101 ## Changes **Non-breaking changes** - Adds... - New component version pavics/thredds-docker:5.5-unidata-2024-11-19-with-tds-plugin-jar-with-dependencies.jar **Breaking changes** - None ## Related Issue / Discussion - Resolves #168 ## Additional Information Links to other issues or sources. <!-- The test suite can be run using a different DACCS config with ``birdhouse_daccs_configs_branch: branch_name`` in the PR description. To globally skip the test suite regardless of the commit message use ``birdhouse_skip_ci: true`` in the PR description. --> birdhouse_daccs_configs_branch: master birdhouse_skip_ci: false
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For Thredds v5 update in bird-house/birdhouse-deploy#413
To fix output change: