HARMPONY-1764: Update pystac and use STAC catalog for sending

operation

Makefile

@@ -30,7 +30,7 @@ lint:
 	flake8 harmony
 
 test:
-	pytest --cov=harmony tests
+	pytest --cov=harmony tests -W ignore::DeprecationWarning
 
 test-no-warnings:
 	pytest --disable-warnings --cov=harmony tests

example/example_message.json

@@ -1,5 +1,5 @@
 {
-  "$schema": "../../harmony/app/schemas/data-operation/0.19.0/data-operation-v0.19.0.json",
+  "$schema": "../../harmony/services/harmony/app/schemas/data-operation/0.19.0/data-operation-v0.19.0.json",
   "version": "0.19.0",
   "callback": "http://localhost/some-path",
   "stagingLocation": "s3://example-bucket/public/some-org/some-service/some-uuid/",

example/source/catalog.json

@@ -1,6 +1,9 @@
 {
-  "stac_version": "1.0.0-beta.2",
-  "stac_extensions": [],
+  "stac_version": "1.0.0",
+  "stac_extensions": [
+    "https://harmony.earthdata.nasa.gov/schemas/stac-extension/0.1.0/schema.json"
+  ],
+  "type": "Catalog",
   "id": "d5addf73-6e95-4ba1-a2a6-528de6d3d22c",
   "links": [
     {

example/source/catalog0.json

@@ -1,6 +1,9 @@
 {
-  "stac_version": "1.0.0-beta.2",
-  "stac_extensions": [],
+  "stac_version": "1.0.0",
+  "stac_extensions": [
+    "https://harmony.earthdata.nasa.gov/schemas/stac-extension/0.1.0/schema.json"
+  ],
+  "type": "Catalog",
   "id": "1bd3924c-c0ee-49b7-b9ac-0d295f4bf909",
   "links": [
     {

example/source/catalog1.json

@@ -1,6 +1,9 @@
 {
-  "stac_version": "1.0.0-beta.2",
-  "stac_extensions": [],
+  "stac_version": "1.0.0",
+  "stac_extensions": [
+    "https://harmony.earthdata.nasa.gov/schemas/stac-extension/0.1.0/schema.json"
+  ],
+  "type": "Catalog",
   "id": "2bd3924c-c0ee-49b7-b9ac-0d296f4af909",
   "links": [
     {

example/source/granule_0_0000000.json

@@ -1,5 +1,5 @@
 {
-  "stac_version": "1.0.0-beta.2",
+  "stac_version": "1.0.0",
   "stac_extensions": [],
   "id": "3ca8ec5a-6d1e-4a82-8233-313d73769e7c",
   "type": "Feature",

example/source/granule_0_0000001.json

@@ -1,5 +1,5 @@
 {
-  "stac_version": "1.0.0-beta.2",
+  "stac_version": "1.0.0",
   "stac_extensions": [],
   "id": "56e7601d-4ff0-445b-85ee-a0174558853e",
   "type": "Feature",

example/source/source_0.json

@@ -1,6 +1,7 @@
 {
-  "stac_version": "1.0.0-beta.2",
+  "stac_version": "1.0.0",
   "stac_extensions": [],
+  "type": "Catalog",
   "id": "8bd3924c-c0ee-49b7-b9ac-0d296f4bf909",
   "links": [
     {

harmony/__init__.py

@@ -12,8 +12,8 @@
 from .adapter import BaseHarmonyAdapter
 from .cli import setup_cli, is_harmony_cli, run_cli
 from .message import Temporal
-from pystac.stac_io import STAC_IO
+from pystac.stac_io import StacIO
 from .s3_stac_io import read, write
 
-STAC_IO.read_text_method = read
-STAC_IO.write_text_method = write
+StacIO.read_text_method = read
+StacIO.write_text_method = write

harmony/adapter.py

@@ -119,6 +119,8 @@ def invoke(self):
         # New-style processing using STAC
         if self.catalog:
             return (self.message, self._process_catalog_recursive(self.catalog))
+        else:
+            warn('===========NO CATALOG ==============', DeprecationWarning, stacklevel=2)
 
         # Deprecated, processing using callbacks
         self._process_with_callbacks()
@@ -167,6 +169,7 @@ def _process_catalog_recursive(self, catalog):
         pystac.Catalog
             A new catalog containing all of the processed results
         """
+        warn('CLONING THE CATALOG', DeprecationWarning, stacklevel=2)
         result = catalog.clone()
         result.id = str(uuid.uuid4())
 

harmony/cli.py

@@ -333,12 +333,13 @@ def run_cli(parser, args, AdapterClass, cfg=None):
             if not successful:
                 raise Exception('Service operation failed')
         else:
-            try:
-                adapter = _build_adapter(AdapterClass,
+            adapter = _build_adapter(AdapterClass,
                                          args.harmony_input,
                                          args.harmony_sources,
                                          args.harmony_data_location,
                                          cfg)
+            try:
+
                 adapter.logger.info(f'timing.{cfg.app_name}.start')
                 _invoke(adapter, args.harmony_metadata_dir)
             finally:

harmony/s3_stac_io.py

@@ -1,6 +1,6 @@
 from urllib.parse import urlparse
 import boto3
-from pystac import STAC_IO
+from pystac.stac_io import DefaultStacIO
 from harmony import util
 from harmony import aws
 from os import environ
@@ -35,7 +35,7 @@ def read(uri):
         obj = s3.Object(bucket, key)
         return obj.get()['Body'].read().decode('utf-8')
     else:
-        return STAC_IO.default_read_text_method(uri)
+        return DefaultStacIO().read_text(uri)
 
 
 def write(uri, txt):
@@ -51,4 +51,4 @@ def write(uri, txt):
     if parsed.scheme == 's3':
         aws.write_s3(uri, txt)
     else:
-        STAC_IO.default_write_text_method(uri, txt)
+        DefaultStacIO().write_text_to_href(uri, txt)

requirements.txt

@@ -1,7 +1,7 @@
 boto3 ~= 1.14
 deprecation ~= 2.1.0
 pynacl ~= 1.4
-pystac ~= 0.5.3
+pystac ~= 1.10.0
 python-json-logger ~= 2.0.1
 requests ~= 2.24
 urllib3 ~= 1.26.9

tests/test_adapter_stac.py

@@ -165,7 +165,7 @@ def test_get_all_items_handles_children(self, test_patch):
         adapter = AdapterTester(message, catalog, config=self.config)
         all_items = list(adapter.get_all_catalog_items(catalog, True))
         self.assertEqual(all_items, [ *items_a, *items_b ])
-        
+
 
     def test_unaltered_ids_are_assigned_new_uuids(self):
         catalog = Catalog('0', 'Catalog 0')
@@ -210,7 +210,8 @@ def test_legacy_invocations_create_stac_catalogs(self):
         self.assertEqual(AdapterTester.process_args[2][1], message.sources[1])
         self.assertEqual(AdapterTester.process_args[0][0].to_dict(), {
             'type': 'Feature',
-            'stac_version': '1.0.0-beta.2',
+            'stac_version': '1.0.0',
+            'stac_extensions': [],
             'id': 'G0001-EXAMPLE',
             'properties': {
                 'start_datetime': '2001-01-01T01:01:01Z',
@@ -230,7 +231,8 @@ def test_legacy_invocations_create_stac_catalogs(self):
         })
         self.assertEqual(AdapterTester.process_args[1][0].to_dict(), {
             'type': 'Feature',
-            'stac_version': '1.0.0-beta.2',
+            'stac_version': '1.0.0',
+            'stac_extensions': [],
             'id': 'G0002-EXAMPLE',
             'properties': {
                 'start_datetime': '2003-03-03T03:03:03Z',