dnastack-client-library 3.1.114a0__py3-none-any.whl → 3.1.120a0__py3-none-any.whl

dnastack/cli/commands/publisher/__init__.py

@@ -1,4 +1,5 @@
 from dnastack.cli.commands.publisher.collections import collections_command_group
+from dnastack.cli.commands.publisher.datasources import datasources_command_group
 from dnastack.cli.core.group import formatted_group
 
 
@@ -8,3 +9,4 @@ def publisher_command_group():
 
 
 publisher_command_group.add_command(collections_command_group)
+publisher_command_group.add_command(datasources_command_group)

dnastack/cli/commands/publisher/datasources/__init__.py

@@ -0,0 +1,9 @@
+from dnastack.cli.core.group import formatted_group
+from dnastack.cli.commands.publisher.datasources.commands import init_datasources_commands
+
+@formatted_group("datasources")
+def datasources_command_group():
+    """ Interact with data sources """
+
+# Initialize all commands
+init_datasources_commands(datasources_command_group)

dnastack/cli/commands/publisher/datasources/commands.py

@@ -0,0 +1,35 @@
+from typing import Optional
+
+from click import Group
+
+from dnastack.cli.commands.publisher.datasources.utils import _get_datasource_client, _filter_datasource_fields
+from dnastack.cli.core.command import formatted_command
+from dnastack.cli.core.command_spec import RESOURCE_OUTPUT_ARG, ArgumentSpec
+from dnastack.cli.helpers.iterator_printer import show_iterator
+from dnastack.common.tracing import Span
+
+def init_datasources_commands(group: Group):
+    @formatted_command(
+        group=group,
+        name='list',
+        specs=[
+            RESOURCE_OUTPUT_ARG,
+            ArgumentSpec(
+                name='type',
+                arg_names=['--type'],
+                help='Filter datasources by type (e.g., "AWS")',
+                required=False
+            ),
+        ]
+    )
+    def list_datasources(output: Optional[str] = None, type: Optional[str] = None):
+        """ List all data sources """
+        with Span("list_datasources") as span:
+            client = _get_datasource_client()
+            response = client.list_datasources(trace=span, type=type)
+
+            show_iterator(output,
+                        [
+                            _filter_datasource_fields(datasource.dict())
+                            for datasource in response.connections
+                        ])

dnastack/cli/commands/publisher/datasources/utils.py

@@ -0,0 +1,18 @@
+from typing import Dict, Any, Optional
+from imagination import container
+from dnastack.cli.helpers.client_factory import ConfigurationBasedClientFactory
+from dnastack.client.datasources.client import DataSourceServiceClient
+
+
+def _get_datasource_client() -> DataSourceServiceClient:
+    """Get the data source service client."""
+    factory: ConfigurationBasedClientFactory = container.get(ConfigurationBasedClientFactory)
+    return factory.get(DataSourceServiceClient)
+
+def _filter_datasource_fields(datasource: Dict[str, Any]) -> Dict[str, Any]:
+    """Filter and transform datasource fields for display."""
+    return {
+        'id': datasource.get('id'),
+        'name': datasource.get('name'),
+        'type': datasource.get('type'),
+    }

dnastack/client/constants.py

@@ -3,6 +3,7 @@ from typing import TypeVar
 from dnastack.client.base_client import BaseServiceClient
 from dnastack.client.collections.client import CollectionServiceClient
 from dnastack.client.data_connect import DataConnectClient
+from dnastack.client.datasources.client import DataSourceServiceClient
 from dnastack.client.drs import DrsClient
 from dnastack.client.service_registry.client import ServiceRegistry
 from dnastack.client.workbench.ewes.client import EWesClient
@@ -15,12 +16,12 @@ from dnastack.client.workbench.workflow.client import WorkflowClient
 ALL_SERVICE_CLIENT_CLASSES = (
     CollectionServiceClient, DataConnectClient, DrsClient, ServiceRegistry, EWesClient, StorageClient, SamplesClient,
     WorkflowClient,
-    WorkbenchUserClient)
+    WorkbenchUserClient, DataSourceServiceClient)
 
 # All client classes for data access
 DATA_SERVICE_CLIENT_CLASSES = (
     CollectionServiceClient, DataConnectClient, DrsClient, EWesClient, StorageClient, WorkflowClient,
-    WorkbenchUserClient)
+    WorkbenchUserClient, DataSourceServiceClient)
 
 # Type variable for the service client
 SERVICE_CLIENT_CLASS = TypeVar('SERVICE_CLIENT_CLASS',
@@ -33,4 +34,5 @@ SERVICE_CLIENT_CLASS = TypeVar('SERVICE_CLIENT_CLASS',
                                DataConnectClient,
                                DrsClient,
                                SamplesClient,
-                               ServiceRegistry)
+                               ServiceRegistry,
+                               DataSourceServiceClient)

dnastack/client/datasources/__init__.py

@@ -0,0 +1,3 @@
+from dnastack.client.datasources.client import DataSource, DataSourcesResponse, DataSourceServiceClient
+
+__all__ = ['DataSourceServiceClient', 'DataSource', 'DataSourcesResponse']

dnastack/client/datasources/client.py

@@ -0,0 +1,124 @@
+from pprint import pformat
+from typing import List, Optional
+from pydantic import BaseModel, ValidationError
+from dnastack.client.base_client import BaseServiceClient
+from dnastack.client.base_exceptions import (
+    UnauthenticatedApiAccessError, UnauthorizedApiAccessError
+)
+from dnastack.client.collections.client import STANDARD_COLLECTION_SERVICE_TYPE_V1_0
+from dnastack.client.collections.model import PageableApiError
+from dnastack.client.datasources.model import DataSource, DataSourceListOptions
+from dnastack.client.result_iterator import ResultLoader, InactiveLoaderError, ResultIterator
+from dnastack.http.session import HttpSession, HttpError
+from dnastack.common.tracing import Span
+
+
+class DataSourcesResponse(BaseModel):
+    connections: List[DataSource]
+
+    def items(self) -> List[DataSource]:
+        return self.connections
+
+class DataSourceListResultLoader(ResultLoader):
+    """
+    Result loader for handling data source fetching without pagination.
+    """
+
+    def __init__(self, service_url: str, http_session: HttpSession, trace: Span,
+                 list_options: Optional[dict] = None, max_results: Optional[int] = None):
+        self.__service_url = service_url
+        self.__http_session = http_session
+        self.__list_options = list_options or {}
+        self.__max_results = max_results
+        self.__loaded_results = 0
+        self.__active = True  # Determines when we are done fetching results
+        self.__trace = trace
+
+    def has_more(self) -> bool:
+        """Checks if there are more results to fetch."""
+        return self.__active
+
+    def extract_api_response(self, response_body: dict) -> DataSourcesResponse:
+        """
+        Converts the API response body into a DataSourcesResponse object.
+        """
+        return DataSourcesResponse(**response_body)
+
+    def load(self) -> List[DataSource]:
+        """Fetches the data from the API."""
+        if not self.__active:
+            raise InactiveLoaderError(self.__service_url)
+
+        with self.__http_session as session:
+            try:
+                # Perform the GET request
+                response = session.get(
+                    self.__service_url,
+                    params=self.__list_options,
+                    trace_context=self.__trace
+                )
+            except HttpError as e:
+                error_feedback = f"Failed to load data from {self.__service_url}: {e.response.text}"
+                if e.response.status_code == 401:
+                    raise UnauthenticatedApiAccessError(error_feedback)
+                elif e.response.status_code == 403:
+                    raise UnauthorizedApiAccessError(error_feedback)
+                else:
+                    raise PageableApiError(error_feedback, e.response.status_code, e.response.text)
+
+            # Parse the API response
+            response_body = response.json() if response.text else {}
+            try:
+                api_response = self.extract_api_response(response_body)
+            except ValidationError:
+                raise PageableApiError(
+                    f"Invalid response body: {response_body}",
+                    response.status_code,
+                    response.text,
+                )
+
+            # Retrieve the data source items
+            items = api_response.items()
+
+            # Deactivate the loader after the first fetch since there's no pagination
+            self.__active = False
+
+            # Handle max_results constraint
+            if self.__max_results and len(items) > self.__max_results:
+                return items[:self.__max_results]
+
+            return items
+
+class DataSourceServiceClient(BaseServiceClient):
+    """
+    Client to interact with the Data Sources API.
+    """
+
+    @staticmethod
+    def get_adapter_type() -> str:
+        return 'collections'
+
+    @classmethod
+    def get_supported_service_types(cls) -> List[str]:
+        """
+        Returns supported service types.
+        """
+        return [ STANDARD_COLLECTION_SERVICE_TYPE_V1_0,]
+
+    def list_datasources(self, type: Optional[str] = None, trace: Optional[Span] = None,
+                         max_results: Optional[int] = None) -> DataSourcesResponse:
+        # Set up query parameters
+        list_options = {}
+        if type:
+            list_options["type"] = type
+
+        trace = trace or Span(origin=self)
+        loader = DataSourceListResultLoader(
+            service_url=f"{self.url}/connections/data-sources",
+            http_session=self.create_http_session(),
+            trace=trace,
+            list_options=list_options,
+            max_results=max_results
+        )
+        connections = list(ResultIterator(loader))
+        return DataSourcesResponse(connections=connections)

dnastack/client/datasources/model.py

@@ -0,0 +1,11 @@
+from typing import Optional
+
+from pydantic.main import BaseModel
+
+class DataSourceListOptions(BaseModel):
+    pass
+
+class DataSource(BaseModel):
+    id: Optional[str]
+    name: Optional[str]
+    type: Optional[str]

dnastack/constants.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "v3.1.114a"
+__version__ = "v3.1.120a"
 
 LOCAL_STORAGE_DIRECTORY = os.path.join(os.path.expanduser("~"), '.dnastack')

{dnastack_client_library-3.1.114a0.dist-info → dnastack_client_library-3.1.120a0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dnastack-client-library
-Version: 3.1.114a0
+Version: 3.1.120a0
 Summary: "DNAstack's GA4GH library and CLI"
 Home-page: https://www.dnastack.com
 Author: DNAstack

{dnastack_client_library-3.1.114a0.dist-info → dnastack_client_library-3.1.120a0.dist-info}/RECORD

@@ -1,6 +1,6 @@
 dnastack/__init__.py,sha256=Bpfm77MeoZNmZHSgDK9wlgVPkcdE73ur6_7Zihorb4o,263
 dnastack/__main__.py,sha256=3rydT8oj5G1IN0asiqv9oaQw2xmyIlVge8c8wUjo0HA,3532
-dnastack/constants.py,sha256=cUGMUqc8saQdOufZDxdRVDtT5y1Rt1VKT4bh1Hz_6HY,115
+dnastack/constants.py,sha256=emInQGO_r53MWwHbI63wDj3e9qlVQaEQ5oP5zP86Qx0,115
 dnastack/feature_flags.py,sha256=RK_V_Ovncoe6NeTheAA_frP-kYkZC1fDlTbbup2KYG4,1419
 dnastack/json_path.py,sha256=TyghhDf7nGQmnsUWBhenU_fKsE_Ez-HLVER6HgH5-hU,2700
 dnastack/omics_cli.py,sha256=ZppKZTHv_XjUUZyRIzSkx0Ug5ODAYrCOTsU0ezCOVrA,3694
@@ -49,12 +49,15 @@ dnastack/cli/commands/dataconnect/utils.py,sha256=7psRouHUsg2QEemZAhzHVsjy1rza63
 dnastack/cli/commands/drs/__init__.py,sha256=XGPfCsdOyZyc67ptYmM903US741hDCKaTowVtysC6H8,325
 dnastack/cli/commands/drs/commands.py,sha256=9n-f24ODZNCpxgIirdzsIEnZqVRw2jFkvXiCsW4ZnOI,5405
 dnastack/cli/commands/drs/utils.py,sha256=tGogaIlXKnk03GqitzeDfo893JlP7Nc_X28sH-yQUrI,427
-dnastack/cli/commands/publisher/__init__.py,sha256=1dILe4uH1omguGjPQYbxMysdxsA2fUy7wvk5hzq41kA,298
+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=gmSCaXXqxk4lElZnqkU6KZCLa5QSDgTd5Zz0LWSBMDQ,6101
 dnastack/cli/commands/publisher/collections/tables.py,sha256=N348MU_p-OKweJwKYtNbpvCD3ZmGGbS-quz7gnsAc1c,2130
 dnastack/cli/commands/publisher/collections/utils.py,sha256=GNgGv29z7eumQqbw1IFFasJeDyxH2KQGQl0q6UPooVU,6244
+dnastack/cli/commands/publisher/datasources/__init__.py,sha256=90suC61lfFF1WzIU9f8lO0_DiLWIQF2Dy46_Yad3CD8,327
+dnastack/cli/commands/publisher/datasources/commands.py,sha256=TdR55CxqlpN62GiHeWIfPfRsorfrzDj7GwZlmBqseA0,1298
+dnastack/cli/commands/publisher/datasources/utils.py,sha256=DGVZY6e0Faa0sNRXxqu50z7kGACX4YYkF-cgtMLaUQc,745
 dnastack/cli/commands/workbench/__init__.py,sha256=H4CGbc31-21mRZqJMtzi2Cg4e_D9a9ibqFjwXQTcXNY,1092
 dnastack/cli/commands/workbench/utils.py,sha256=V2I192k4XAg2h-DrsdatqIZfguflh6WR7q5pSBojUX0,4354
 dnastack/cli/commands/workbench/engines/__init__.py,sha256=qB1rfGXNJ6_N6F5UYXos4hHDwhm8PtlbrCCt_uNhIIw,653
@@ -103,7 +106,7 @@ dnastack/cli/helpers/printer.py,sha256=IdGoEnBWtzgPAE2KLoZEfwshn0tkrTu-XXtN-KXj8
 dnastack/client/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/base_client.py,sha256=ZhaWHHTQcuPun6RdrtCdShGRYoY18hEKAIHmr8Z728M,3730
 dnastack/client/base_exceptions.py,sha256=QoYa-LzT5C0o7eq6Ek4R_-clBL0nZ5v7qdFBcCoUiw4,2888
-dnastack/client/constants.py,sha256=vV4ea5WrYJeCIfcC6YcNfh6F16SauFjBG2dhkupwAek,1672
+dnastack/client/constants.py,sha256=6nB1QKz-GEx8BSnPLFafKGG1WDF3l0P0_HlC01FSvwc,1849
 dnastack/client/data_connect.py,sha256=6qDx6-dl-fmakEMYK_jfTgUcYe1yl8eTCMPI_8tRUwg,26211
 dnastack/client/drs.py,sha256=7iNu58YAtQHKFFFNllFyXATfasT_ndkgSkBKKgDbiKc,21225
 dnastack/client/factory.py,sha256=PQGYUGhKeqyJtEtc-bZM5OlEup9K7lB-qwmNiII_4HU,6288
@@ -112,6 +115,9 @@ dnastack/client/result_iterator.py,sha256=00zEs7YbPJyt8d-6j7eHnmSVurP8hIOarj4Fws
 dnastack/client/collections/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/collections/client.py,sha256=ea7N7fDP5jdyPT3_gwd3WVm_wsGZ4ApTm6qdUr3X70k,15376
 dnastack/client/collections/model.py,sha256=JO-eC_jc7hY9PBvST3x1vkmJE0LPDAbcUq5VBKcGyLM,3492
+dnastack/client/datasources/__init__.py,sha256=HxDIHuQX8KMWr3o70ucL3x79pXKaIHbBq7JqmyoRGxM,179
+dnastack/client/datasources/client.py,sha256=AfYxu18QRLh3tNe6uwS_Z00VwZCZNw7fUYMsEDDMe40,4734
+dnastack/client/datasources/model.py,sha256=dV9Sf05ivIq0ubwIIYK3kSv1xJ_TtjxvVp_ddI9aHEk,214
 dnastack/client/service_registry/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dnastack/client/service_registry/client.py,sha256=r7D8CnPJLbNkc03g2PYHt880Ba1oPW2d8B0ShP0p4Eo,1131
 dnastack/client/service_registry/factory.py,sha256=l_H4ipFzv9j6VkWoPtyHOHJvCCmS6ceVpazjD5qfXM0,10741
@@ -177,9 +183,9 @@ dnastack/http/authenticators/oauth2_adapter/client_credential.py,sha256=cCVZa4B1
 dnastack/http/authenticators/oauth2_adapter/device_code_flow.py,sha256=_OMHPf7qekPn_oSCBb41iYg9100sQMVzfJiKZHdh26w,6529
 dnastack/http/authenticators/oauth2_adapter/factory.py,sha256=r8K6swt5zhraP74KhTL2K4sQ71HWAMLM0oHg8qQT4BA,965
 dnastack/http/authenticators/oauth2_adapter/models.py,sha256=U11r8DZsWvjIRNCJE1mmQMuprZw3fpFwFBg7vmI5w48,660
-dnastack_client_library-3.1.114a0.dist-info/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
-dnastack_client_library-3.1.114a0.dist-info/METADATA,sha256=c0GocQcklX10DyFUQqapEvE9FRjeObALAsTgBLA0YAU,968
-dnastack_client_library-3.1.114a0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-dnastack_client_library-3.1.114a0.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
-dnastack_client_library-3.1.114a0.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
-dnastack_client_library-3.1.114a0.dist-info/RECORD,,
+dnastack_client_library-3.1.120a0.dist-info/LICENSE,sha256=uwybO-wUbQhxkosgjhJlxmYATMy-AzoULFO9FUedE34,11580
+dnastack_client_library-3.1.120a0.dist-info/METADATA,sha256=6fbWkDqg_o_lE-mKC7oDKWMkqeqKlHl3s8dDDdsKBeU,968
+dnastack_client_library-3.1.120a0.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+dnastack_client_library-3.1.120a0.dist-info/entry_points.txt,sha256=Y6OeicsiyGn3-8D-SiV4NiKlJgXfkSqK88kFBR6R1rY,89
+dnastack_client_library-3.1.120a0.dist-info/top_level.txt,sha256=P2RgRyqJ7hfNy1wLVRoVLJYEppUVkCX3syGK9zBqkt8,9
+dnastack_client_library-3.1.120a0.dist-info/RECORD,,

{dnastack_client_library-3.1.114a0.dist-info → dnastack_client_library-3.1.120a0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any