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Make item geometry and bbox nullable for sqlalchemy backend
Closes #350
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-6
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7 files changed

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‎CHANGES.md

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([#355](https://github.com/stac-utils/stac-fastapi/issues/355))
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* docker-compose now runs uvicorn with hot-reloading enabled
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* Bump version of PGStac to 0.6.2 that includes support for hydrating results in the API backed ([#397](https://github.com/stac-utils/stac-fastapi/pull/397))
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* Make item geometry and bbox nullable in sqlalchemy backend. ([#398](https://github.com/stac-utils/stac-fastapi/pull/398))
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### Removed
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‎stac_fastapi/sqlalchemy/alembic/versions/7016c1bf3fbf_make_item_geometry_and_bbox_nullable.py

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"""Make item geometry and bbox nullable
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Revision ID: 7016c1bf3fbf
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Revises: 5909bd10f2e6
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Create Date: 2022-04-28 10:40:06.856826
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"""
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from alembic import op
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# revision identifiers, used by Alembic.
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revision = "7016c1bf3fbf"
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down_revision = "5909bd10f2e6"
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branch_labels = None
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depends_on = None
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def upgrade():
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op.alter_column(
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schema="data",
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table_name="items",
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column_name="geometry",
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nullable=True,
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)
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op.alter_column(
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schema="data",
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table_name="items",
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column_name="bbox",
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nullable=True,
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)
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def downgrade():
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# Downgrading will require the user to update or remove all null geometry
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# cases from the DB, otherwise the downgrade migration will fail.
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op.alter_column(
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schema="data",
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table_name="items",
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column_name="geometry",
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nullable=False,
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)
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op.alter_column(
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schema="data",
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table_name="items",
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column_name="bbox",
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nullable=False,
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)

‎stac_fastapi/sqlalchemy/setup.py

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@@ -8,7 +8,7 @@
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install_requires = [
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"attrs",
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"pydantic[dotenv]",
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"stac_pydantic==2.0.*",
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"stac_pydantic>=2.0.3",
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"stac-fastapi.types",
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"stac-fastapi.api",
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"stac-fastapi.extensions",

‎stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/models/database.py

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@@ -64,8 +64,10 @@ class Item(BaseModel): # type:ignore
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id = sa.Column(sa.VARCHAR(1024), nullable=False, primary_key=True)
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stac_version = sa.Column(sa.VARCHAR(300))
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stac_extensions = sa.Column(sa.ARRAY(sa.VARCHAR(300)), nullable=True)
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geometry = sa.Column(GeojsonGeometry("GEOMETRY", srid=4326, spatial_index=True))
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bbox = sa.Column(sa.ARRAY(sa.NUMERIC), nullable=False)
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geometry = sa.Column(
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GeojsonGeometry("GEOMETRY", srid=4326, spatial_index=True), nullable=True
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)
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bbox = sa.Column(sa.ARRAY(sa.NUMERIC), nullable=True)
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properties = sa.Column(JSONB)
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assets = sa.Column(JSONB)
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collection_id = sa.Column(

‎stac_fastapi/sqlalchemy/stac_fastapi/sqlalchemy/serializers.py

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@@ -78,14 +78,18 @@ def db_to_stac(cls, db_model: database.Item, base_url: str) -> stac_types.Item:
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if isinstance(geometry, str):
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geometry = json.loads(geometry)
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bbox = db_model.bbox
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if bbox is not None:
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bbox = [float(x) for x in db_model.bbox]
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return stac_types.Item(
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type="Feature",
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stac_version=db_model.stac_version,
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stac_extensions=stac_extensions,
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id=db_model.id,
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collection=db_model.collection_id,
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geometry=geometry,
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bbox=[float(x) for x in db_model.bbox],
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bbox=bbox,
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properties=properties,
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links=item_links,
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assets=db_model.assets,
@@ -111,13 +115,17 @@ def stac_to_db(
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stac_data["properties"]["created"] = now
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stac_data["properties"]["updated"] = now
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geometry = stac_data["geometry"]
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if geometry is not None:
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geometry = json.dumps(geometry)
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return database.Item(
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id=stac_data["id"],
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collection_id=stac_data["collection"],
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stac_version=stac_data["stac_version"],
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stac_extensions=stac_data.get("stac_extensions"),
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geometry=json.dumps(stac_data["geometry"]),
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bbox=stac_data["bbox"],
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geometry=geometry,
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bbox=stac_data.get("bbox"),
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properties=stac_data["properties"],
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assets=stac_data["assets"],
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**indexed_fields,

‎stac_fastapi/sqlalchemy/tests/api/test_api.py

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@@ -92,6 +92,21 @@ def test_app_search_response_multipolygon(
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assert resp_json.get("features")[0]["geometry"]["type"] == "MultiPolygon"
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def test_app_search_response_geometry_null(
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load_test_data, app_client, postgres_transactions
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):
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item = load_test_data("test_item_geometry_null.json")
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postgres_transactions.create_item(item, request=MockStarletteRequest)
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resp = app_client.get("/search", params={"collections": ["test-collection"]})
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assert resp.status_code == 200
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resp_json = resp.json()
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assert resp_json.get("type") == "FeatureCollection"
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assert resp_json.get("features")[0]["geometry"] is None
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assert resp_json.get("features")[0]["bbox"] is None
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def test_app_context_extension(load_test_data, app_client, postgres_transactions):
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item = load_test_data("test_item.json")
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postgres_transactions.create_item(item, request=MockStarletteRequest)

‎stac_fastapi/sqlalchemy/tests/data/test_item_geometry_null.json

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{
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"type": "Feature",
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"stac_version": "1.0.0",
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"stac_extensions": [
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"https://landsat.usgs.gov/stac/landsat-ard-extension/v1.0.0/schema.json",
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"https://stac-extensions.github.io/projection/v1.0.0/schema.json",
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"https://stac-extensions.github.io/eo/v1.0.0/schema.json",
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"https://stac-extensions.github.io/alternate-assets/v1.1.0/schema.json",
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"https://stac-extensions.github.io/storage/v1.0.0/schema.json"
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],
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"id": "LE07_CU_002012_20150101_20210502_02_BA",
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"description": "Landsat Collection 2 Level-3 Burned Area Product",
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"geometry": null,
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"properties": {
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"datetime": "2015-01-01T18:39:12.4885358Z",
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"platform": "LANDSAT_7",
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"instruments": [
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"ETM"
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],
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"landsat:grid_horizontal": "02",
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"landsat:grid_vertical": "12",
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"landsat:grid_region": "CU",
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"landsat:scene_count": 1,
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"eo:cloud_cover": 0.0759,
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"landsat:cloud_shadow_cover": 0.1394,
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"landsat:snow_ice_cover": 0,
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"landsat:fill": 95.4286,
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"proj:epsg": null,
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"proj:shape": [
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5000,
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5000
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],
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"proj:transform": [
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30,
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0,
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-2265585,
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0,
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-30,
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1514805
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],
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"created": "2022-02-08T20:07:38.885Z",
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"updated": "2022-02-08T20:07:38.885Z"
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},
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"assets": {
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"index": {
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"title": "HTML index page",
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"type": "text/html",
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"roles": [
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"metadata"
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],
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"href": "https://landsatlook.usgs.gov/stac-browser/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02"
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},
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"bp": {
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"title": "Burn Probability",
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"description": "Collection 2 Level-3 Albers Burn Probability Burned Area",
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"type": "image/vnd.stac.geotiff; cloud-optimized=true",
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"roles": [
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"data"
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],
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"href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BP.TIF",
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"alternate": {
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"s3": {
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"storage:platform": "AWS",
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"storage:requester_pays": true,
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"href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BP.TIF"
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}
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}
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},
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"bc": {
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"title": "Burn Classification",
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"description": "Collection 2 Level-3 Albers Burn Classification Burned Area",
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"type": "image/vnd.stac.geotiff; cloud-optimized=true",
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"roles": [
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"data"
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],
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"href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BC.TIF",
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"alternate": {
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"s3": {
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"storage:platform": "AWS",
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"storage:requester_pays": true,
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"href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_BC.TIF"
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}
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}
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},
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"quick_look": {
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"title": "Quick Look File",
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"description": "Collection 2 Level-3 Albers Quick Look File Burned Area",
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"type": "image/png",
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"roles": [
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"data"
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],
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"href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_QuickLook.png",
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"alternate": {
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"s3": {
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"storage:platform": "AWS",
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"storage:requester_pays": true,
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"href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02_QuickLook.png"
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}
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}
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},
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"xml": {
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"title": "Extensible Metadata File",
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"description": "Collection 2 Level-3 Albers Extensible Metadata File Burned Area",
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"type": "application/xml",
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"roles": [
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"metadata"
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],
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"href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.xml",
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"alternate": {
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"s3": {
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"storage:platform": "AWS",
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"storage:requester_pays": true,
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"href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.xml"
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}
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}
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},
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"json": {
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"title": "Extensible Metadata File (json)",
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"description": "Collection 2 Level-3 Albers Extensible Metadata File (json) Burned Area",
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"type": "application/json",
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"roles": [
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"metadata"
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],
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"href": "https://landsatlook.usgs.gov/level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.json",
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"alternate": {
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"s3": {
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"storage:platform": "AWS",
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"storage:requester_pays": true,
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"href": "s3://usgs-landsat-level-3/collection02/BA/2015/CU/002/012/LE07_CU_002012_20150101_20210502_02_BA/LE07_CU_002012_20150101_20210502_02.json"
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}
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}
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}
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},
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"links": [
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{
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"rel": "self",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba/items/LE07_CU_002012_20150101_20210502_02_BA"
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},
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{
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"rel": "derived_from",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-sr/items/LE07_CU_002012_20150101_20210502_02_SR"
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},
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{
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"rel": "derived_from",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-st/items/LE07_CU_002012_20150101_20210502_02_ST"
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},
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{
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"rel": "derived_from",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-ta/items/LE07_CU_002012_20150101_20210502_02_TOA"
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},
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{
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"rel": "derived_from",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2ard-bt/items/LE07_CU_002012_20150101_20210502_02_BT"
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},
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{
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"rel": "parent",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba"
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},
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{
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"rel": "collection",
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"href": "https://landsatlook.usgs.gov/stac-server/collections/landsat-c2l3-ba"
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},
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{
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"rel": "root",
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"href": "https://landsatlook.usgs.gov/stac-server/"
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}
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],
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"collection": "test-collection"
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}

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