Not working with the GEOBON STAC catalogue

[tpoisot]

The following is empty:

using STAC
catalog = STAC.Catalog("https://stac.geobon.org/")
entry = catalog["chelsa-clim"]

Specifically, the output is

julia> entry = catalog["chelsa-clim"]
chelsa-clim
CHELSA Climatologies
CHELSA Climatologies
License: CC-BY-SA-4.0

But using the URL gives a list of the expected items withing this collection: https://stac.geobon.org/collections/chelsa-clim/items

Is there something I am missing?

[Alexander-Barth]

Thanks for the reproducer.
The code is looking for item (without the endings s):

STAC.jl/src/catalog.jl

Line 118 in e163edb

listi = filter(l -> l[:rel] == "item",data[:links])

In stac.geobon.org's JSON however, the rel field has the value items (with an s):

julia> entry = catalog["chelsa-clim"];

julia> entry.data.links
4-element JSON3.Array{JSON3.Object, Base.CodeUnits{UInt8, String}, SubArray{UInt64, 1, Vector{UInt64}, Tuple{UnitRange{Int64}}, true}}:
 {
    "rel": "items",
   "type": "application/geo+json",
   "href": "https://stac.geobon.org/collections/chelsa-clim/items"
}
 {
    "rel": "parent",
   "type": "application/json",
   "href": "https://stac.geobon.org/"
}
 {
    "rel": "root",
   "type": "application/json",
   "href": "https://stac.geobon.org/"
}
 {
    "rel": "self",
   "type": "application/json",
   "href": "https://stac.geobon.org/collections/chelsa-clim"
}

See the spec:
https://github.com/radiantearth/stac-spec/blob/2e6947df194a707354d6d5be1da6762647ee593f/commons/links.md#link-object

and example:

https://github.com/radiantearth/stac-spec/blob/2e6947df194a707354d6d5be1da6762647ee593f/examples/collection.json#L93

Does the spec also mentions items in plural for the rel field?

[tpoisot]

Thanks @Alexander-Barth -- you are right, neither the spec nor the types for link relations in IANA use items

@jmlord / @glaroc -- it seems that the GEOBON STAC catalogue isn't following the spec

[glaroc]

We are using STAC Fastapi. This might be a difference between STAC spec and STAC API spec ? Other catalogs I'm looking at use items with an "s".

https://planetarycomputer.microsoft.com/api/stac/v1/collections/terraclimate
https://eocat.esa.int/eo-catalogue/collections

[tpoisot]

Yeah, the STAC API spec is different from the STAC spec 😕

[Alexander-Barth]

That would be a real bummer. The STAC spec is already quite extensive as is. Or maybe it is an extension (https://stac-extensions.github.io/) or a beta version of the spec (just a speculation). Maybe the raising an issue at https://github.com/radiantearth/stac-spec/ would help?

[glaroc]

In any case, if catalogs like the Planetary Computer and ESA have items instead of item, this library should probably support it. Otherwise, many users will face similar issues. The rstac R package and the Python pystac library work fine with our catalog.

[Alexander-Barth]

Are you able to read the items with pystac? This is what I tried, but I got also an empty list for the items.

import pystac
root_catalog = pystac.Catalog.from_file("https://stac.geobon.org/")

root_catalog.get_child("chelsa-clim").title
# output 'CHELSA Climatologies'

list(root_catalog.get_child("chelsa-clim").get_items())
# output []

list(root_catalog.get_child("chelsa-clim").get_items(recursive=True))
# output []

pystac.__version__
# output '1.10.1'

I am not very familiar with pystac, I followed the documentation here https://pystac.readthedocs.io/en/stable/quickstart.html#Crawling-Items

[glaroc]

@Alexander-Barth I believe you have to use pystac_client: https://pystac-client.readthedocs.io/en/latest/usage.html

Static and dynamic catalogs have different characteristics. For example, sub-catalogs are not allowed with the STAC API Spec, while they are in the STAC Spec. I guess items vs item is another difference.

[Alexander-Barth]

This seems to be relevant:

https://github.com/radiantearth/stac-api-spec/blob/604ade6158de15b8ab068320ca41e25e2bf0e116/overview.md?plain=1#L40

[Alexander-Barth]

This should be fixed in the current main branch:

julia> using STAC
Precompiling STAC
  1 dependency successfully precompiled in 3 seconds. 41 already precompiled.

julia> catalog = STAC.Catalog("https://stac.geobon.org/")
geobon-stac
BON in a Box STAC
Spatio Temporal Asset Catalog for layers used in BON in a Box, courtesy of GEO BON.
Children:
   * chelsa-clim: CHELSA Climatologies
   * gfw-lossyear: Global Forest Watch - Loss year
   * soilgrids: Soil Grids datasets
   * ghmts: Global Human Modification of Terrestrial Systems
   * gfw-treecover2000: Global Forest Watch - Tree cover 2000
   * gfw-gain: Global Forest Watch - Gain
   * chelsa-monthly: CHELSA monthly timeseries
   * esacci-lc: ESA Land cover time series
   * chelsa-clim-proj: CHELSA Climatologies Projections
   * silvis: Silvis Dynamic Habitat Indices
   * colombia-lc: Colombian land cover time series
   * earthenv_topography: EarthEnv - Topography
   * earthenv_landcover: EarthEnv - Consensus Land Cover - Full version
   * earthenv_habitat_heterogeneity: EarthEnv - Habitat heterogeneity
   * accessibility_to_cities: Accessibility - Time to access cities
   * colombia_forests: Time series of the presence of forests in Colombia
   * qc_pilot_env: Environmental layers for the Quebec pilot BON optimization project.
   * global-mammals: Global habitat availability for mammals from 2015-2055
   * fragmentation-rmf: Relative Magnitude of Fragmentation (RMF)
   * colombia-human-footprint: Colombia - Human Footprint
   * colombia-protected-areas: Colombia - Protected Areas
   * earthenv_topography_derived: EarthEnv - Derived topographic categorical variables
   * distance_to_roads: Distance to roads
   * cec_land_cover: CEC North American Land Cover
   * gbif_heatmaps: Occurrence density maps created from GBIF data
   * cec_land_cover_percentage: CEC North American Land Cover Percentage at 300 m resolution
   * cec_derived_maps: Rasters derived from CEC North American Land Cover map to serve as inputs for various pipelines.
   * ncp_cna: Nature's Contribution to People - Critical Natural Assets


julia> entry = catalog["chelsa-clim"]
chelsa-clim
CHELSA Climatologies
CHELSA Climatologies
License: CC-BY-SA-4.0
Items:
   * bio9
   * bio8
   * bio7
   * bio6
   * bio5
   * bio4
   * bio3
   * bio2
   * bio19
   * bio18
   * bio17
   * bio16
   * bio15
   * bio14
   * bio13
   * bio12
   * bio11
   * bio10
   * bio1


julia> entry.items["bio1"]
bio1
bounding box:
    ┌────── 83.99986───────┐
    │                      │
-180.00014              179.99986
    │                      │
    └──────-90.00014───────┘

date time: 1981-01-01T00:00:00
Assets:
   * bio1


julia> entry.items["bio1"].assets["bio1"]
type: image/tiff; application=geotiff; profile=cloud-optimized
href: https://object-arbutus.cloud.computecanada.ca/bq-io/io/CHELSA/climatologies/CHELSA_bio1_1981-2010_V.2.1.tif

STAC.jl should now also support the item-search extension.

[tpoisot]

AMAZING! Thank you so much!!!!

[Alexander-Barth]

Great! I am closing the issue and will soon make a new release.