dnastack-client-library 3.1.204__py3-none-any.whl → 3.1.207__py3-none-any.whl

dnastack/cli/commands/publisher/collections/commands.py

@@ -174,17 +174,9 @@ def init_collections_commands(group: Group):
         name='status',
         specs=[
             COLLECTION_ID_ARG,
-            ArgumentSpec(
-                name='missing_items',
-                arg_names=['--missing-items'],
-                help='To find missing files and/or folders while adding or removing to the collection.',
-                type=bool,
-                required=False,
-            ),
         ]
     )
-    def get_collection_status(collection: str,
-                            missing_items: Optional[bool] = False):
+    def get_collection_status(collection: str):
         """ Check status of a collection """
 
         def format_datetime(dt: Optional[datetime]) -> str:
@@ -193,6 +185,16 @@ def init_collections_commands(group: Group):
                 return dt.strftime("%Y-%m-%d %H:%M:%S")
             return "N/A"
 
+        def get_status_color(status: CollectionValidationStatus) -> str:
+            """Get color for status based on validation state"""
+            status_colors = {
+                CollectionValidationStatus.VALIDATED: 'green',
+                CollectionValidationStatus.VALIDATION_STOPPED: 'red',
+                CollectionValidationStatus.VALIDATION_IN_PROGRESS: 'yellow',
+                CollectionValidationStatus.MISSING_ITEMS: 'yellow'
+            }
+            return status_colors.get(status, 'white')
+
         def format_validation_status(status: CollectionValidationStatus) -> str:
             """Convert enum status to user-friendly message"""
             status_messages = {
@@ -207,29 +209,27 @@ def init_collections_commands(group: Group):
             """Print hint about missing items to stderr"""
             hint = (
                 "# Run the following command to see details.\n"
-                f"omics publisher collections status --collection {collection_id} --missing-items"
+                f"omics publisher collections items list --collection {collection_id} --missing-items"
             )
-            click.echo(hint, err=True)
+            click.secho(hint, dim=True, err=True)
 
         def format_collection_status(status: CollectionStatus, collection_id: str) -> None:
             """Format and print collection status according to requirements"""
-            # Print main status
-            click.echo(f"Validation Status: {format_validation_status(status.validationsStatus)}")
+            # Print main status with color
+            status_color = get_status_color(status.validationsStatus)
+            click.echo("Validation Status: ", nl=False)
+            click.secho(format_validation_status(status.validationsStatus), fg=status_color)
 
             if status.lastChecked:
                 click.echo(f"Last Checked: {format_datetime(status.lastChecked)}")
 
-            # Print missing items if any
+            # Print missing items count if any
             if status.validationsStatus == CollectionValidationStatus.MISSING_ITEMS and status.missingItems:
-                click.echo("\nMissing Items:")
-                if status.missingItems.tables:
-                    click.echo(f"  Tables: {status.missingItems.tables}")
-                if status.missingItems.files:
-                    click.echo(f"  Files: {status.missingItems.files}")
+                click.echo("\nNumber of Missing Items: ", nl=False)
+                click.secho(str(status.missingItems), fg='yellow', bold=True)
                 click.echo()  # Add empty line before stderr message
                 print_missing_items_hint(collection_id)
 
         client = _get_collection_service_client()
         status = client.get_collection_status(collection_id_or_slug_name_or_db_schema_name=collection)
-
         format_collection_status(status, collection)

dnastack/cli/commands/publisher/collections/items.py

@@ -40,6 +40,13 @@ def items_command_group():
             help='The type of items to list.',
             required=False,
         ),
+        ArgumentSpec(
+            name='missing_items',
+            arg_names=['--missing-items'],
+            help='List only missing items from the collection.',
+            type=bool,
+            required=False,
+        ),
         MAX_RESULTS_ARG,
         RESOURCE_OUTPUT_ARG
     ]
@@ -48,6 +55,7 @@ def list(collection: str,
          limit: Optional[int],
          max_results: Optional[int],
          item_type: Optional[str],
+         missing_items: Optional[bool] = False,
          output: Optional[str] = None):
     """ List items of the given collection """
     assert limit >= 0, 'The limit (--limit) should be either ZERO (item query WITHOUT limit) ' \
@@ -56,6 +64,7 @@ def list(collection: str,
     list_options = CollectionItemListOptions(
         type=item_type,
         limit=limit,
+        onlyMissing=missing_items if missing_items else None,
     )
 
     collection_service_client = _get_collection_service_client()

dnastack/client/collections/model.py

@@ -105,6 +105,7 @@ class CollectionItemListResponse(BaseModel):
 class CollectionItemListOptions(BaseModel):
     type: Optional[str] = None
     limit: Optional[int] = None
+    onlyMissing: Optional[bool] = None
 
 
 class CreateCollectionItemsRequest(BaseModel):

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "3.1.204"
+__version__ = "3.1.207"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

dnastack/http/authenticators/factory.py

@@ -1,10 +1,11 @@
 from typing import List, Any, Dict, Optional
+import logging
 
 from dnastack.client.models import ServiceEndpoint
 from dnastack.common.model_mixin import JsonModelMixin
 from dnastack.http.authenticators.abstract import Authenticator
 from dnastack.http.authenticators.oauth2 import OAuth2Authenticator
-from dnastack.http.authenticators.oauth2_adapter.models import OAuth2Authentication
+from dnastack.http.authenticators.oauth2_adapter.models import OAuth2Authentication, SUPPORTED_GRANT_TYPES
 
 
 class UnsupportedAuthenticationInformationError(RuntimeError):
@@ -43,10 +44,21 @@ class HttpAuthenticatorFactory:
 
     @staticmethod
     def get_unique_auth_info_list(endpoints: List[ServiceEndpoint]) -> List[Dict[str, Any]]:
+        logger = logging.getLogger(__name__)
         unique_auth_info_map: Dict[str, Dict[str, Any]] = {}
 
         for endpoint in endpoints:
             for auth_info in endpoint.get_authentications():
+                grant_type = auth_info.get('grant_type')
+
+                # Skip authentication methods with unsupported grant types
+                if grant_type and grant_type not in SUPPORTED_GRANT_TYPES:
+                    logger.debug("Skipping authentication with unsupported grant type '{}' for resource '{}'".format(
+                        grant_type,
+                        auth_info.get('resource_url', 'unknown')
+                    ))
+                    continue
+
                 unique_auth_info_map[JsonModelMixin.hash(auth_info)] = auth_info
 
         return sorted(unique_auth_info_map.values(), key=lambda a: a.get('resource_url') or a.get('type'))

dnastack/http/authenticators/oauth2.py

@@ -130,7 +130,7 @@ class OAuth2Authenticator(Authenticator):
             self.events.dispatch('authentication-failure', event_details)
 
             raise OAuth2MisconfigurationError('Cannot determine the type of authentication '
-                                              f'({auth_info.json(sort_keys=True, exclude_none=True)})')
+                                              f'({auth_info.model_dump_json(exclude_none=True)})')
 
         adapter.check_config_readiness()
         for auth_event_type in ['blocking-response-required', 'blocking-response-ok', 'blocking-response-failed']:

dnastack/http/authenticators/oauth2_adapter/models.py

@@ -6,6 +6,15 @@ from dnastack.common.model_mixin import JsonModelMixin as HashableModel
 
 
 GRANT_TYPE_TOKEN_EXCHANGE = 'urn:ietf:params:oauth:grant-type:token-exchange'
+GRANT_TYPE_DEVICE_CODE = 'urn:ietf:params:oauth:grant-type:device_code'
+GRANT_TYPE_CLIENT_CREDENTIALS = 'client_credentials'
+
+# List of grant types supported by the CLI
+SUPPORTED_GRANT_TYPES = [
+    GRANT_TYPE_DEVICE_CODE,
+    GRANT_TYPE_CLIENT_CREDENTIALS,
+    GRANT_TYPE_TOKEN_EXCHANGE,
+]
 
 
 class OAuth2Authentication(BaseModel, HashableModel):

{dnastack_client_library-3.1.204.dist-info → dnastack_client_library-3.1.207.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dnastack-client-library
-Version: 3.1.204
+Version: 3.1.207
 Summary: DNAstack's GA4GH library and CLI
 Author-email: DNAstack <devs@dnastack.com>
 License: Apache License, Version 2.0

{dnastack_client_library-3.1.204.dist-info → dnastack_client_library-3.1.207.dist-info}/RECORD

@@ -1,6 +1,6 @@
 dnastack/__init__.py,sha256=mslf7se8vBSK_HkqWTGPdibeVhT4xyKXgzQBV7dEK1M,333
 dnastack/__main__.py,sha256=EKmtIs4TBseQJi-OT_U6LqRyKLiyrGTBuTQg9zE-G2I,4376
-dnastack/constants.py,sha256=K3XY21O6eakBvFiJHP9tzHHSBP4YLYDzlBPE3IdCfcY,113
+dnastack/constants.py,sha256=ATOtsE118-FzkYW3GE1qbxQMUBSg9xDjPCGSqbHtQtA,113
 dnastack/feature_flags.py,sha256=UMNDB07R_ep6Fx3iClhzwOpkWfyYnb418FpoJo50CGs,1411
 dnastack/json_path.py,sha256=TyghhDf7nGQmnsUWBhenU_fKsE_Ez-HLVER6HgH5-hU,2700
 dnastack/omics_cli.py,sha256=ZppKZTHv_XjUUZyRIzSkx0Ug5ODAYrCOTsU0ezCOVrA,3694
@@ -57,8 +57,8 @@ dnastack/cli/commands/explorer/questions/tables.py,sha256=cb8YKqY7Qxrm2ROz7z8H6b
 dnastack/cli/commands/explorer/questions/utils.py,sha256=Np3AARD6ZSl2Ywvpsa4UJxw1Ark7D5NqgwPp1OopL54,8000
 dnastack/cli/commands/publisher/__init__.py,sha256=G8WNdx1UwanoA4X349ghv8Zyv5YizB8ryeJmwu9px8o,443
 dnastack/cli/commands/publisher/collections/__init__.py,sha256=KmclN_KY3ctVhtv-i8rxXpWTshPCj1tY6yhud4vrXYQ,636
-dnastack/cli/commands/publisher/collections/commands.py,sha256=A82NphvnD-9JuN2dVU_07EbAvB1NE7Em07IU7eDhagc,9454
-dnastack/cli/commands/publisher/collections/items.py,sha256=6V8w0wugRYQIwBSqHoYhkzJyiA5Bp5uDhg7tvxMa-9A,6040
+dnastack/cli/commands/publisher/collections/commands.py,sha256=dM6l8ickhoxBYgAiGbLHNnej-UwjhmBvEAGbBALftLA,9622
+dnastack/cli/commands/publisher/collections/items.py,sha256=JKmoZn6yOJdf2TzjCXV1aq5mNtE4SKU7RW3P9OQSMvo,6376
 dnastack/cli/commands/publisher/collections/tables.py,sha256=8_lKjpSyhqJ8EzYzF3Qcht7hErp8kOfZykpAJDg3uUo,2136
 dnastack/cli/commands/publisher/collections/utils.py,sha256=6_w7lX5LyEagdKt1DLWz84cTviZF9SN-VIe2JPti_XE,6250
 dnastack/cli/commands/publisher/datasources/__init__.py,sha256=90suC61lfFF1WzIU9f8lO0_DiLWIQF2Dy46_Yad3CD8,327
@@ -122,7 +122,7 @@ dnastack/client/models.py,sha256=_vOVpyfCaO0tQBIbESG3IUxAFv0Cix8jfXRn1ul1Rb4,290
 dnastack/client/result_iterator.py,sha256=00zEs7YbPJyt8d-6j7eHnmSVurP8hIOarj4FwsiR7xc,1908
 dnastack/client/collections/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/collections/client.py,sha256=fg3qVyVRqufW8kwM3jtQVz4zzNoHjuW9DtCzSykg-mw,16011
-dnastack/client/collections/model.py,sha256=NUDCXt2WcT8RTQoRtzHzFpWKK-GztkasdeyeyYkGUu8,3695
+dnastack/client/collections/model.py,sha256=VFuzE7ebWvuyR52RFa3Bod2Twje1JUBTz_7jLnsA5ms,3734
 dnastack/client/datasources/__init__.py,sha256=HxDIHuQX8KMWr3o70ucL3x79pXKaIHbBq7JqmyoRGxM,179
 dnastack/client/datasources/client.py,sha256=jfVzCSKuQJsggbvfJVbftYJ0hd6gAPsBZMgvINOgjRE,4671
 dnastack/client/datasources/model.py,sha256=QdZ7tn0Zn4BJPGdyRSwGDu2AmsBCg74j7stGZL0pIuU,235
@@ -188,19 +188,19 @@ dnastack/http/session_info.py,sha256=7Fny2U1Zixab4CFGwNsn8Am4tNKYYHF7C1ERG3BhHBI
 dnastack/http/authenticators/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/http/authenticators/abstract.py,sha256=Q74LnZwsMKs5TfGI_4oZtXBCpgJKkkimkv_Y8YPHuoM,9246
 dnastack/http/authenticators/constants.py,sha256=mSpBnm5lMMmMJwr13KIfCoOXXJLP4qGDkFprYXALu8o,1278
-dnastack/http/authenticators/factory.py,sha256=Kt6PH0-Umfa4ah-Jn8fZthUp2XXKyguhebj3-B0fAZc,2064
-dnastack/http/authenticators/oauth2.py,sha256=yZ_bBaIVscDZC25f2vwBptkdcLwX47nFakhL6PW28lM,20071
+dnastack/http/authenticators/factory.py,sha256=zjV5xMZKlkKqUHA2QDXmut-2HxTnqAz8vwxTBEkMg60,2627
+dnastack/http/authenticators/oauth2.py,sha256=FKAoCCt_s9XmtVcOJpdll09XSU-lqxne_VO3zqm2DkE,20066
 dnastack/http/authenticators/oauth2_adapter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/http/authenticators/oauth2_adapter/abstract.py,sha256=Tm4Nnroo5_vp0UgZHhcEDVRRbhIrvVdfPr8nTyihoH4,2832
 dnastack/http/authenticators/oauth2_adapter/client_credential.py,sha256=2iVOof4YZEVGizDRDBISbv8U_xIemtUnHzzxa3mxswc,2770
 dnastack/http/authenticators/oauth2_adapter/cloud_providers.py,sha256=UHQ-YHHr5ipqSQVzCfr95Uv3zkFcop_RCpK4q6a2yJg,4317
 dnastack/http/authenticators/oauth2_adapter/device_code_flow.py,sha256=dXI5CyUcsqYg6gf5vDC_3eY6Cc-H1C8W7FeD_24j92A,6750
 dnastack/http/authenticators/oauth2_adapter/factory.py,sha256=ZtNXOklWEim-26ooNoPp3ji_hRg1vf4fHHnY94F0wLI,1087
-dnastack/http/authenticators/oauth2_adapter/models.py,sha256=Dry1supZCVe4aR_0mGdVry5Ctwnvz_mpa1wsGZYloCw,1048
+dnastack/http/authenticators/oauth2_adapter/models.py,sha256=7UsC8DkStMBx7Bz_xHQNi_J1UO_H4nfHme7oBhokj2I,1339
 dnastack/http/authenticators/oauth2_adapter/token_exchange.py,sha256=nSuAsSKWa_UNqHSbPMOEk4komaFITYAnE04Sk5WOrLc,6332
-dnastack_client_library-3.1.204.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.204.dist-info/METADATA,sha256=AhgGt7wY9BE1btWg41L806nbYLLS8LtOAtuD8o4URx0,1761
-dnastack_client_library-3.1.204.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dnastack_client_library-3.1.204.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.204.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.204.dist-info/RECORD,,
+dnastack_client_library-3.1.207.dist-info/licenses/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.207.dist-info/METADATA,sha256=plCNoaEWQp1W31XbH_9uJFvo-N1vqxKTVHjg0YYfddo,1761
+dnastack_client_library-3.1.207.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dnastack_client_library-3.1.207.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.207.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.207.dist-info/RECORD,,