diff --git a/catalog/catalog.json b/catalog/catalog.json
index db6fd2178820e75e2c003bd3f306716d92aa114f..12dade7382ae5dd9d4645ac8b7de07f555a5f115 100644
--- a/catalog/catalog.json
+++ b/catalog/catalog.json
@@ -29,11 +29,6 @@
"href": "./alaska_et_2020_gfdl_historical_simulation/collection.json",
"type": "application/json"
},
- {
- "rel": "child",
- "href": "./cprep_tasmax_day_I35txdetrp1-DeltaSD-A12L01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
- "type": "application/json"
- },
{
"rel": "child",
"href": "./macav2_historical_daily/collection.json",
@@ -318,6 +313,11 @@
"rel": "child",
"href": "./notaro_MRI_2080_2099/collection.json",
"type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep/collection.json",
+ "type": "application/json"
}
]
-}
\ No newline at end of file
+}
diff --git a/catalog/cprep/collection.json b/catalog/cprep/collection.json
new file mode 100644
index 0000000000000000000000000000000000000000..27de05f81700e67ca9187c866a1ed6baf3882803
--- /dev/null
+++ b/catalog/cprep/collection.json
@@ -0,0 +1,1524 @@
+{
+ "type": "Collection",
+ "id": "cprep",
+ "stac_version": "1.0.0",
+ "description": "South Central Climate Projections Evaluation Project (C-PrEP)",
+ "links": [
+ {
+ "rel": "root",
+ "href": "../catalog.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_tasmax_day_I35txdetrp1-DeltaSD-A38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "parent",
+ "href": "../catalog.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A12D01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A12L01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A12P01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A14D01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A14L01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A14P01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A18D01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A18L01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A18P01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A22D01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A22L01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A22P01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A24D01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A24L01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A24P01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A28D01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A28L01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A28P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A32D01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A32L01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A32P01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A34D01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A34L01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A34P01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A38D01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A38L01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-DeltaSD-A38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B10D01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B10L01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B10P01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B12D01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B12L01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B12P01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B14D01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B14L01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B14P01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B18D01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B18L01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B18P01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B20D01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B20L01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B20P01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B22D01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B22L01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B22P01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B24D01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B24L01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B24P01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B28D01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B28L01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B28P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B30D01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B30L01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B30P01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B32D01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B32L01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B32P01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B34D01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B34L01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B34P01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B38D01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B38L01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-PARM-B38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A10D01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A10L01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A10P01K00_historical_r6i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A12D01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A12L01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A12P01K00_rcp26_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A14D01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A14L01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A14P01K00_rcp45_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A18D01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A18L01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A18P01K00_rcp85_r6i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A20D01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A20L01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A20P01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A22D01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A22L01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A22P01K00_rcp26_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A24D01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A24L01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A24P01K00_rcp45_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A28D01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A28L01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A28P01K00_rcp85_r1i1p1_I35Land_20060101-20991231/collection.json",
+ "type": "application/json"
+ },
+ {
+ "rel": "child",
+ "href": "./cprep_pr_day_I35prp1-QDM-A30D01K00_historical_r1i1p1_I35Land_19810101-20051231/collection.json",
+ "type": "application/json"
+ },
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+ "temporal": {
+ "interval": [
+ [
+ "2006-01-01T12:00:00Z",
+ "2099-12-31T12:00:00Z"
+ ]
+ ]
+ }
+ },
+ "license": "Unlicense",
+ "assets": {
+ "zarr-s3-osn": {
+ "href": "s3://mdmf/gdp/cprep/cprep_tasmin_day_I35tnp1-EDQM-A38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231.zarr/",
+ "type": "application/vnd+zarr",
+ "description": "Open Storage Network Pod S3 API access to collection zarr group",
+ "xarray:open_kwargs": {
+ "chunks": {},
+ "engine": "zarr",
+ "consolidated": true
+ },
+ "xarray:storage_options": {
+ "anon": true,
+ "client_kwargs": {
+ "endpoint_url": "https://usgs.osn.mghpcc.org/"
+ }
+ },
+ "roles": [
+ "data",
+ "zarr",
+ "s3"
+ ]
+ },
+ "zarr-s3": {
+ "href": "s3://nhgf-development/workspace/DataConversion/gdp/cprep/cprep_tasmin_day_I35tnp1-EDQM-A38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231.zarr/",
+ "type": "application/vnd+zarr",
+ "description": "S3 access to collection zarr group",
+ "xarray:open_kwargs": {
+ "chunks": {},
+ "engine": "zarr",
+ "consolidated": true
+ },
+ "xarray:storage_options": {
+ "requester_pays": true
+ },
+ "roles": [
+ "data",
+ "zarr",
+ "s3"
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/workflows/archive/cprep_create_collection_from_zarr.ipynb b/workflows/archive/cprep_create_collection_from_zarr.ipynb
index df0be7b8d2d3dae9878db12a38cfe38f8b70f929..1ed26c7c90223f71e2269a694d3a4c5bce4bcd45 100644
--- a/workflows/archive/cprep_create_collection_from_zarr.ipynb
+++ b/workflows/archive/cprep_create_collection_from_zarr.ipynb
@@ -119,7 +119,10 @@
"outputs": [],
"source": [
"# name for STAC collection\n",
- "collection_id = os.path.splitext(zarr_list[100])[0]"
+ "# most of them look like this one\n",
+ "collection_id = os.path.splitext(zarr_list[100])[0]\n",
+ "# this one fails on decode times\n",
+ "collection_id = \"cprep_tasmax_day_I35txdetrp1-DeltaSD-A38P01K00_rcp85_r1i1p1_I35Land_20060101-20991231\""
]
},
{
@@ -197,8 +200,10 @@
"source": [
"# open and view zarr dataset\n",
"fs2 = fsspec.filesystem('s3', anon=True, endpoint_url='https://usgs.osn.mghpcc.org/')\n",
+ "# ds = xr.open_dataset(fs2.get_mapper(zarr_url), engine='zarr', \n",
+ "# backend_kwargs={'consolidated':True}, chunks={})\n",
"ds = xr.open_dataset(fs2.get_mapper(zarr_url), engine='zarr', \n",
- " backend_kwargs={'consolidated':True}, chunks={})\n",
+ " backend_kwargs={'consolidated':True}, chunks={}, decode_times=False)\n",
"ds"
]
},
@@ -430,10 +435,10 @@
"outputs": [],
"source": [
"# pull out first and last timestamps\n",
- "# temporal_extent_lower = pd.Timestamp(ds[dim_names_dict['T']].data.min())\n",
- "# temporal_extent_upper = pd.Timestamp(ds[dim_names_dict['T']].data.max())\n",
- "temporal_extent_lower = ds.indexes[dim_names_dict['T']].to_datetimeindex().min()\n",
- "temporal_extent_upper = ds.indexes[dim_names_dict['T']].to_datetimeindex().max()\n",
+ "temporal_extent_lower = pd.Timestamp(ds[dim_names_dict['T']].data.min())\n",
+ "temporal_extent_upper = pd.Timestamp(ds[dim_names_dict['T']].data.max())\n",
+ "# temporal_extent_lower = ds.indexes[dim_names_dict['T']].to_datetimeindex().min()\n",
+ "# temporal_extent_upper = ds.indexes[dim_names_dict['T']].to_datetimeindex().max()\n",
"print(f'min: {temporal_extent_lower} \\nmax: {temporal_extent_upper}')\n",
"# create a temporal extent object\n",
"temporal_extent = pystac.TemporalExtent(intervals=[[temporal_extent_lower, temporal_extent_upper]])"
@@ -476,6 +481,60 @@
"catalog = pystac.Catalog.from_file(os.path.join(catalog_path, 'catalog.json'))"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e56853f8-1cb1-46ea-b6ee-5c9295b20311",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "#create cprep overall collection\n",
+ "# note: each dataset has the same spatial extent, so the extent extracted from one dataset is used here\n",
+ "# 241 ocurrences: \n",
+ "# min: 2006-01-01 12:00:00\n",
+ "# max: 2099-12-31 12:00:00\n",
+ "# 54 occurences:\n",
+ "# min: 1981-01-01 12:00:00 \n",
+ "# max: 2005-12-31 12:00:00\n",
+ "# 2 occurrences\n",
+ "# min: 1970-01-01 00:00:00.000016425 \n",
+ "# max: 1983-11-03 21:13:54.048972992\n",
+ "overall_temporal_extent= pystac.TemporalExtent(intervals=[[pd.Timestamp('1970-01-01 00:00:00.000016425'), pd.Timestamp('2099-12-31 12:00:00')]])\n",
+ "overall_collection_extent = pystac.Extent(spatial=spatial_extent, temporal=overall_temporal_extent)\n",
+ "overall_collection_id = 'cprep'\n",
+ "collection_extent\n",
+ "if catalog.get_child(overall_collection_id):\n",
+ " cprep_collection = catalog.get_child(overall_collection_id)\n",
+ " print(\"existing collection opened\")\n",
+ " cprep_collection.extent=overall_collection_extent\n",
+ " cprep_collection.description=collection_description\n",
+ " cprep_collection.license=collection_license\n",
+ "else:\n",
+ " cprep_collection = pystac.Collection(id=overall_collection_id,\n",
+ " description=collection_description,\n",
+ " extent=overall_collection_extent,\n",
+ " license=collection_license)\n",
+ " print(\"new collection created\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "f039d8aa-f385-4660-a662-dfe363cc25b2",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "if catalog.get_child(overall_collection_id):\n",
+ " cprep_collection.normalize_and_save(root_href=os.path.join(catalog_path, overall_collection_id), catalog_type=pystac.CatalogType.SELF_CONTAINED)\n",
+ "else:\n",
+ " catalog.add_child(cprep_collection)\n",
+ " catalog.normalize_and_save(root_href=catalog_path, catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -485,7 +544,8 @@
},
"outputs": [],
"source": [
- "if catalog.get_child(collection_id):\n",
+ "# create collection for current zarr\n",
+ "if cprep_collection.get_child(collection_id):\n",
" collection = catalog.get_child(collection_id)\n",
" print(\"existing collection opened\")\n",
" collection.extent=collection_extent\n",
@@ -641,6 +701,8 @@
"outputs": [],
"source": [
"time_step = pd.Timedelta(stac_helpers.get_step(ds, dim_names_dict['T'], time_dim=True)).isoformat()\n",
+ "if time_step=='NaT' and ((ds.isel(time=1).time - ds.isel(time=0).time)==1) and (ds.time.units=='days since 1961-01-01 00:00'):\n",
+ " time_step=\"P1DT0H0M0S\"\n",
"print(f'time step: {time_step}')"
]
},
@@ -938,17 +1000,19 @@
"metadata": {},
"outputs": [],
"source": [
- "if catalog.get_child(collection_id):\n",
+ "if cprep_collection.get_child(collection_id):\n",
" collection.normalize_and_save(root_href=os.path.join(catalog_path, collection_id), catalog_type=pystac.CatalogType.SELF_CONTAINED)\n",
"else:\n",
- " catalog.add_child(collection)\n",
- " catalog.normalize_and_save(root_href=catalog_path, catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+ " cprep_collection.add_child(collection)\n",
+ " cprep_collection.normalize_and_save(root_href=catalog_path+f'/{overall_collection_id}', catalog_type=pystac.CatalogType.SELF_CONTAINED)"
]
},
{
"cell_type": "markdown",
"id": "c734db5d-a9b4-42b4-88fb-50d84493f694",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
"## The big job\n",
"Now that we have tested the workflow, we will implement it in a big for loop for all 297 zarrs."
@@ -960,6 +1024,226 @@
"id": "929a90d4-2ae1-480a-aec3-348d19a667d8",
"metadata": {},
"outputs": [],
+ "source": [
+ "fs2 = fsspec.filesystem('s3', anon=True, endpoint_url='https://usgs.osn.mghpcc.org/')\n",
+ "\n",
+ "# define folder location where your STAC catalog json file is\n",
+ "catalog_path = os.path.join('..', '..', 'catalog')\n",
+ "# open catalog\n",
+ "catalog = pystac.Catalog.from_file(os.path.join(catalog_path, 'catalog.json'))\n",
+ "\n",
+ "for zarr in zarr_list:\n",
+ " collection_id = os.path.splitext(zarr)[0]\n",
+ " \n",
+ " # url to zarr store that you want to create a collection for\n",
+ " zarr_url = f's3://mdmf/gdp/cprep/{collection_id}.zarr/'\n",
+ "\n",
+ " # define keyword arguments needed for opening the dataset with xarray\n",
+ " # ref: https://github.com/stac-extensions/xarray-assets\n",
+ " xarray_opendataset_kwargs = {\"xarray:open_kwargs\":{\"chunks\":{},\"engine\":\"zarr\",\"consolidated\":True},\n",
+ " \"xarray:storage_options\": {\"anon\": True, \"client_kwargs\": {\"endpoint_url\":\"https://usgs.osn.mghpcc.org/\"}}}\n",
+ " # description for zarr url asset attached to collection (zarr_url)\n",
+ " asset_description = \"Open Storage Network Pod S3 API access to collection zarr group\"\n",
+ " # roles to tag zarr url asset with\n",
+ " asset_roles = [\"data\",\"zarr\",\"s3\"]\n",
+ " \n",
+ " # url to zarr store that you want to create a collection for\n",
+ " zarr_url2 = f's3://nhgf-development/workspace/DataConversion/gdp/cprep/{collection_id}.zarr/'\n",
+ "\n",
+ " # define keyword arguments needed for opening the dataset with xarray\n",
+ " # ref: https://github.com/stac-extensions/xarray-assets\n",
+ " xarray_opendataset_kwargs2 = {\"xarray:open_kwargs\":{\"chunks\":{},\"engine\":\"zarr\",\"consolidated\":True},\n",
+ " \"xarray:storage_options\":{\"requester_pays\":True}}\n",
+ " # description for zarr url asset attached to collection (zarr_url)\n",
+ " asset_description2 = \"S3 access to collection zarr group\"\n",
+ " # roles to tag zarr url asset with\n",
+ " asset_roles2 = [\"data\",\"zarr\",\"s3\"]\n",
+ " \n",
+ " # open and view zarr dataset\n",
+ " try:\n",
+ " ds = xr.open_dataset(fs2.get_mapper(zarr_url), engine='zarr', \n",
+ " backend_kwargs={'consolidated':True}, chunks={})\n",
+ " decode_times=True\n",
+ "\n",
+ " except:\n",
+ " ds = xr.open_dataset(fs2.get_mapper(zarr_url), engine='zarr', \n",
+ " backend_kwargs={'consolidated':True}, chunks={}, decode_times=False)\n",
+ " decode_times=False\n",
+ " \n",
+ " # description of STAC collection\n",
+ " collection_description = ds.attrs['title']\n",
+ " \n",
+ " # license for dataset\n",
+ " collection_license = stac_helpers.license_picker(ds.attrs['license'])\n",
+ " \n",
+ " dims_auto_extract = ['X', 'Y', 'T']\n",
+ " dim_names_dict = {}\n",
+ " for d in dims_auto_extract:\n",
+ " dim_names_dict[d] = stac_helpers.extract_dim(ds, d)\n",
+ " \n",
+ " crs_var = 'crs'\n",
+ " # use pyproj to automatically extract crs info\n",
+ " crs = pyproj.CRS.from_cf(ds[crs_var].attrs)\n",
+ " \n",
+ " # create a spatial extent object \n",
+ " spatial_bounds = [ds[dim_names_dict['X']].data.min().astype(float).item(), ds[dim_names_dict['Y']].data.min().astype(float).item(), ds[dim_names_dict['X']].data.max().astype(float).item(), ds[dim_names_dict['Y']].data.max().astype(float).item()]\n",
+ " XX, YY = np.meshgrid(ds[dim_names_dict['X']].data, ds[dim_names_dict['Y']].data)\n",
+ " transformer = Transformer.from_crs(crs, \"EPSG:4326\", always_xy=True)\n",
+ " lon, lat = transformer.transform(XX.ravel(), YY.ravel())\n",
+ " print(f'lower left coordinates (WGS84): {min(lon)}, {min(lat)}')\n",
+ " print(f'upper right coordinates (WGS84): {max(lon)}, {max(lat)}')\n",
+ " spatial_extent = pystac.SpatialExtent(bboxes=[[min(lon).item(), min(lat).item(), max(lon).item(), max(lat).item()]])\n",
+ " \n",
+ " # pull out first and last timestamps\n",
+ " if decode_times:\n",
+ " temporal_extent_lower = ds.indexes[dim_names_dict['T']].to_datetimeindex().min()\n",
+ " temporal_extent_upper = ds.indexes[dim_names_dict['T']].to_datetimeindex().max()\n",
+ " else:\n",
+ " temporal_extent_lower = pd.Timestamp(ds[dim_names_dict['T']].data.min())\n",
+ " temporal_extent_upper = pd.Timestamp(ds[dim_names_dict['T']].data.max())\n",
+ " print(f'min: {temporal_extent_lower} \\nmax: {temporal_extent_upper}')\n",
+ " # create a temporal extent object\n",
+ " temporal_extent = pystac.TemporalExtent(intervals=[[temporal_extent_lower, temporal_extent_upper]])\n",
+ " \n",
+ " collection_extent = pystac.Extent(spatial=spatial_extent, temporal=temporal_extent)\n",
+ " \n",
+ " # create collection for current zarr\n",
+ " if cprep_collection.get_child(collection_id):\n",
+ " collection = catalog.get_child(collection_id)\n",
+ " print(\"existing collection opened\")\n",
+ " collection.extent=collection_extent\n",
+ " collection.description=collection_description\n",
+ " collection.license=collection_license\n",
+ " else:\n",
+ " collection = pystac.Collection(id=collection_id,\n",
+ " description=collection_description,\n",
+ " extent=collection_extent,\n",
+ " license=collection_license)\n",
+ " print(\"new collection created\")\n",
+ " \n",
+ " asset_id = \"zarr-s3-osn\"\n",
+ " asset = pystac.Asset(href=zarr_url,\n",
+ " description=asset_description,\n",
+ " media_type=\"application/vnd+zarr\",\n",
+ " roles=asset_roles,\n",
+ " extra_fields = xarray_opendataset_kwargs)\n",
+ " collection.add_asset(asset_id, asset)\n",
+ " \n",
+ " asset_id2 = \"zarr-s3\"\n",
+ " asset2 = pystac.Asset(href=zarr_url2,\n",
+ " description=asset_description2,\n",
+ " media_type=\"application/vnd+zarr\",\n",
+ " roles=asset_roles2,\n",
+ " extra_fields = xarray_opendataset_kwargs2)\n",
+ " collection.add_asset(asset_id2, asset2)\n",
+ " \n",
+ " # instantiate extention on collection\n",
+ " dc = DatacubeExtension.ext(collection, add_if_missing=True)\n",
+ " \n",
+ " # list out dataset dimensions\n",
+ " dims = list(ds.dims)\n",
+ " \n",
+ " projjson = crs.to_json()\n",
+ "\n",
+ " time_step = pd.Timedelta(stac_helpers.get_step(ds, dim_names_dict['T'], time_dim=True)).isoformat()\n",
+ " x_step = stac_helpers.get_step(ds, dim_names_dict['X'], round_dec=13)\n",
+ " y_step = stac_helpers.get_step(ds, dim_names_dict['Y'], round_dec=13)\n",
+ " print(f'x step: {x_step}')\n",
+ " print(f'y step: {y_step}')\n",
+ " \n",
+ " # create a dictionary of datacube dimensions you would like to assign to this dataset\n",
+ " dims_dict = {dim_names_dict['T']: pystac.extensions.datacube.Dimension({'type': 'temporal', 'description': stac_helpers.get_long_name(ds, dim_names_dict['T']), 'extent': [temporal_extent_lower.strftime('%Y-%m-%dT%XZ'), temporal_extent_upper.strftime('%Y-%m-%dT%XZ')], 'step':time_step}),\n",
+ " dim_names_dict['X']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'x', 'description': stac_helpers.get_long_name(ds, dim_names_dict['X']), 'extent': [spatial_bounds[0], spatial_bounds[2]], 'step': x_step, 'reference_system': projjson}),\n",
+ " dim_names_dict['Y']: pystac.extensions.datacube.Dimension({'type': 'spatial', 'axis': 'y', 'description': stac_helpers.get_long_name(ds, dim_names_dict['Y']), 'extent': [spatial_bounds[1], spatial_bounds[3]], 'step': y_step, 'reference_system': projjson}),\n",
+ " 'bnds': pystac.extensions.datacube.Dimension({'type': 'count', 'description': stac_helpers.get_long_name(ds, 'bnds'), 'extent': [ds.bnds.min().item(), ds.bnds.max().item()]}),\n",
+ " }\n",
+ " # make sure you added all the right dims\n",
+ " assert sorted(list(dims_dict.keys())) == sorted(dims)\n",
+ " \n",
+ " # drop metpy_crs coordinate we have added\n",
+ " if 'metpy_crs' in ds.coords:\n",
+ " ds = ds.drop_vars('metpy_crs')\n",
+ "\n",
+ " # pull list of vars from dataset\n",
+ " vars = list(ds.variables)\n",
+ "\n",
+ " # spec says that the keys of cube:dimensions and cube:variables should be unique together; a key like lat should not be both a dimension and a variable.\n",
+ " # we will drop all values in dims from vars\n",
+ " vars = [v for v in vars if v not in dims]\n",
+ "\n",
+ " # Microsoft Planetary Computer includes coordinates and crs as variables here:\n",
+ " # https://planetarycomputer.microsoft.com/dataset/daymet-annual-na\n",
+ " # https://planetarycomputer.microsoft.com/api/stac/v1/collections/daymet-annual-na\n",
+ " # we will keep those in the var list\n",
+ "\n",
+ " # create dictionary of dataset variables and associated dimensions\n",
+ " vars_dict={}\n",
+ " for v in vars:\n",
+ " unit = stac_helpers.get_unit(ds, v)\n",
+ " var_type = stac_helpers.get_var_type(ds, v, crs_var)\n",
+ " long_name = stac_helpers.get_long_name(ds, v)\n",
+ " vars_dict[v] = pystac.extensions.datacube.Variable({'dimensions':list(ds[v].dims), 'type': var_type, 'description': long_name, 'unit': unit})\n",
+ " \n",
+ " # add dimesions and variables to collection extension\n",
+ " dc.apply(dimensions=dims_dict, variables=vars_dict)\n",
+ " \n",
+ " if cprep_collection.get_child(collection_id):\n",
+ " collection.normalize_and_save(root_href=os.path.join(catalog_path, collection_id), catalog_type=pystac.CatalogType.SELF_CONTAINED)\n",
+ " else:\n",
+ " cprep_collection.add_child(collection)\n",
+ " cprep_collection.normalize_and_save(root_href=catalog_path+f'/{overall_collection_id}', catalog_type=pystac.CatalogType.SELF_CONTAINED)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "ca1bd339-a580-48fe-af4e-c1de7c8cbc48",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "zarr_url"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "334d826f-df7f-4b9c-82de-1354352945f0",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "a60045a8-1496-47e0-9d3d-e4bf02bbfbc6",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1e68c395-5cc2-478e-bfb9-57e2bc22a47c",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "9cbfd7ae-5eda-46be-a978-7b9e32306cb2",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b868cf72-86a6-4fc0-84a6-58633700e2eb",
+ "metadata": {},
+ "outputs": [],
"source": []
},
{