cirro-api-client 0.3.2__tar.gz → 1.0.0__tar.gz

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cirro_api_client
-Version: 0.3.2
+Version: 1.0.0
 Summary: A client library for accessing Cirro
 License: MIT
 Keywords: Cirro

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/cirro_api_client/cirro_client.py

@@ -49,6 +49,8 @@ class CirroApiClient(Client):
     raise_on_unexpected_status: bool = field(default=True, kw_only=True)
     client_name: str = field(kw_only=True, default="Cirro API Client")
     package_name: str = field(kw_only=True, default="cirro-api-client")
+    user_agent: str = field(init=False, default=None)
 
     def __attrs_post_init__(self):
-        self._headers["User-Agent"] = _get_user_agent(self.package_name, self.client_name)
+        self.user_agent = _get_user_agent(self.package_name, self.client_name)
+        self._headers["User-Agent"] = self.user_agent

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/cirro_api_client/v1/api/governance/get_requirements.py

@@ -1,18 +1,28 @@
 from http import HTTPStatus
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import httpx
 
 from ... import errors
 from ...client import Client
 from ...models.governance_requirement import GovernanceRequirement
-from ...types import Response
+from ...types import UNSET, Response, Unset
 
 
-def _get_kwargs() -> Dict[str, Any]:
+def _get_kwargs(
+    *,
+    project_id: Union[Unset, str] = UNSET,
+) -> Dict[str, Any]:
+    params: Dict[str, Any] = {}
+
+    params["projectId"] = project_id
+
+    params = {k: v for k, v in params.items() if v is not UNSET and v is not None}
+
     _kwargs: Dict[str, Any] = {
         "method": "get",
         "url": "/governance/requirements",
+        "params": params,
     }
 
     return _kwargs
@@ -44,11 +54,16 @@ def _build_response(*, client: Client, response: httpx.Response) -> Response[Lis
 def sync_detailed(
     *,
     client: Client,
+    project_id: Union[Unset, str] = UNSET,
 ) -> Response[List["GovernanceRequirement"]]:
     """Get requirements
 
      Retrieve a list of governance requirements
 
+    Args:
+        project_id (Union[Unset, str]):
+        client (Client): instance of the API client
+
     Raises:
         errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
         httpx.TimeoutException: If the request takes longer than Client.timeout.
@@ -57,7 +72,9 @@ def sync_detailed(
         Response[List['GovernanceRequirement']]
     """
 
-    kwargs = _get_kwargs()
+    kwargs = _get_kwargs(
+        project_id=project_id,
+    )
 
     response = client.get_httpx_client().request(
         auth=client.get_auth(),
@@ -70,11 +87,16 @@ def sync_detailed(
 def sync(
     *,
     client: Client,
+    project_id: Union[Unset, str] = UNSET,
 ) -> Optional[List["GovernanceRequirement"]]:
     """Get requirements
 
      Retrieve a list of governance requirements
 
+    Args:
+        project_id (Union[Unset, str]):
+        client (Client): instance of the API client
+
     Raises:
         errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
         httpx.TimeoutException: If the request takes longer than Client.timeout.
@@ -86,6 +108,7 @@ def sync(
     try:
         return sync_detailed(
             client=client,
+            project_id=project_id,
         ).parsed
     except errors.NotFoundException:
         return None
@@ -94,11 +117,16 @@ def sync(
 async def asyncio_detailed(
     *,
     client: Client,
+    project_id: Union[Unset, str] = UNSET,
 ) -> Response[List["GovernanceRequirement"]]:
     """Get requirements
 
      Retrieve a list of governance requirements
 
+    Args:
+        project_id (Union[Unset, str]):
+        client (Client): instance of the API client
+
     Raises:
         errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
         httpx.TimeoutException: If the request takes longer than Client.timeout.
@@ -107,7 +135,9 @@ async def asyncio_detailed(
         Response[List['GovernanceRequirement']]
     """
 
-    kwargs = _get_kwargs()
+    kwargs = _get_kwargs(
+        project_id=project_id,
+    )
 
     response = await client.get_async_httpx_client().request(auth=client.get_auth(), **kwargs)
 
@@ -117,11 +147,16 @@ async def asyncio_detailed(
 async def asyncio(
     *,
     client: Client,
+    project_id: Union[Unset, str] = UNSET,
 ) -> Optional[List["GovernanceRequirement"]]:
     """Get requirements
 
      Retrieve a list of governance requirements
 
+    Args:
+        project_id (Union[Unset, str]):
+        client (Client): instance of the API client
+
     Raises:
         errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
         httpx.TimeoutException: If the request takes longer than Client.timeout.
@@ -134,6 +169,7 @@ async def asyncio(
         return (
             await asyncio_detailed(
                 client=client,
+                project_id=project_id,
             )
         ).parsed
     except errors.NotFoundException:

cirro_api_client-1.0.0/cirro_api_client/v1/api/metadata/get_dataset_samples.py

@@ -0,0 +1,181 @@
+from http import HTTPStatus
+from typing import Any, Dict, List, Optional
+
+import httpx
+
+from ... import errors
+from ...client import Client
+from ...models.sample import Sample
+from ...types import Response
+
+
+def _get_kwargs(
+    project_id: str,
+    dataset_id: str,
+) -> Dict[str, Any]:
+    _kwargs: Dict[str, Any] = {
+        "method": "get",
+        "url": f"/projects/{project_id}/datasets/{dataset_id}/samples",
+    }
+
+    return _kwargs
+
+
+def _parse_response(*, client: Client, response: httpx.Response) -> Optional[List["Sample"]]:
+    if response.status_code == HTTPStatus.OK:
+        response_200 = []
+        _response_200 = response.json()
+        for response_200_item_data in _response_200:
+            response_200_item = Sample.from_dict(response_200_item_data)
+
+            response_200.append(response_200_item)
+
+        return response_200
+
+    errors.handle_error_response(response, client.raise_on_unexpected_status)
+
+
+def _build_response(*, client: Client, response: httpx.Response) -> Response[List["Sample"]]:
+    return Response(
+        status_code=HTTPStatus(response.status_code),
+        content=response.content,
+        headers=response.headers,
+        parsed=_parse_response(client=client, response=response),
+    )
+
+
+def sync_detailed(
+    project_id: str,
+    dataset_id: str,
+    *,
+    client: Client,
+) -> Response[List["Sample"]]:
+    """Get dataset samples
+
+     Retrieves a list of samples associated with a dataset along with their metadata
+
+    Args:
+        project_id (str):
+        dataset_id (str):
+        client (Client): instance of the API client
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[List['Sample']]
+    """
+
+    kwargs = _get_kwargs(
+        project_id=project_id,
+        dataset_id=dataset_id,
+    )
+
+    response = client.get_httpx_client().request(
+        auth=client.get_auth(),
+        **kwargs,
+    )
+
+    return _build_response(client=client, response=response)
+
+
+def sync(
+    project_id: str,
+    dataset_id: str,
+    *,
+    client: Client,
+) -> Optional[List["Sample"]]:
+    """Get dataset samples
+
+     Retrieves a list of samples associated with a dataset along with their metadata
+
+    Args:
+        project_id (str):
+        dataset_id (str):
+        client (Client): instance of the API client
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        List['Sample']
+    """
+
+    try:
+        return sync_detailed(
+            project_id=project_id,
+            dataset_id=dataset_id,
+            client=client,
+        ).parsed
+    except errors.NotFoundException:
+        return None
+
+
+async def asyncio_detailed(
+    project_id: str,
+    dataset_id: str,
+    *,
+    client: Client,
+) -> Response[List["Sample"]]:
+    """Get dataset samples
+
+     Retrieves a list of samples associated with a dataset along with their metadata
+
+    Args:
+        project_id (str):
+        dataset_id (str):
+        client (Client): instance of the API client
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        Response[List['Sample']]
+    """
+
+    kwargs = _get_kwargs(
+        project_id=project_id,
+        dataset_id=dataset_id,
+    )
+
+    response = await client.get_async_httpx_client().request(auth=client.get_auth(), **kwargs)
+
+    return _build_response(client=client, response=response)
+
+
+async def asyncio(
+    project_id: str,
+    dataset_id: str,
+    *,
+    client: Client,
+) -> Optional[List["Sample"]]:
+    """Get dataset samples
+
+     Retrieves a list of samples associated with a dataset along with their metadata
+
+    Args:
+        project_id (str):
+        dataset_id (str):
+        client (Client): instance of the API client
+
+    Raises:
+        errors.UnexpectedStatus: If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.
+        httpx.TimeoutException: If the request takes longer than Client.timeout.
+
+    Returns:
+        List['Sample']
+    """
+
+    try:
+        return (
+            await asyncio_detailed(
+                project_id=project_id,
+                dataset_id=dataset_id,
+                client=client,
+            )
+        ).parsed
+    except errors.NotFoundException:
+        return None

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/cirro_api_client/v1/api/processes/create_custom_process.py

@@ -6,15 +6,15 @@ import httpx
 from ... import errors
 from ...client import Client
 from ...models.create_response import CreateResponse
+from ...models.custom_process_input import CustomProcessInput
 from ...models.error_message import ErrorMessage
 from ...models.portal_error_response import PortalErrorResponse
-from ...models.process_detail import ProcessDetail
 from ...types import Response
 
 
 def _get_kwargs(
     *,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Dict[str, Any]:
     headers: Dict[str, Any] = {}
 
@@ -65,14 +65,14 @@ def _build_response(
 def sync_detailed(
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Response[Union[CreateResponse, ErrorMessage, PortalErrorResponse]]:
     """Create custom process
 
      Creates a custom data type or pipeline which you can use in the listed projects.
 
     Args:
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:
@@ -98,14 +98,14 @@ def sync_detailed(
 def sync(
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Optional[Union[CreateResponse, ErrorMessage, PortalErrorResponse]]:
     """Create custom process
 
      Creates a custom data type or pipeline which you can use in the listed projects.
 
     Args:
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:
@@ -128,14 +128,14 @@ def sync(
 async def asyncio_detailed(
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Response[Union[CreateResponse, ErrorMessage, PortalErrorResponse]]:
     """Create custom process
 
      Creates a custom data type or pipeline which you can use in the listed projects.
 
     Args:
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:
@@ -158,14 +158,14 @@ async def asyncio_detailed(
 async def asyncio(
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Optional[Union[CreateResponse, ErrorMessage, PortalErrorResponse]]:
     """Create custom process
 
      Creates a custom data type or pipeline which you can use in the listed projects.
 
     Args:
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/cirro_api_client/v1/api/processes/update_custom_process.py

@@ -5,14 +5,14 @@ import httpx
 
 from ... import errors
 from ...client import Client
-from ...models.process_detail import ProcessDetail
+from ...models.custom_process_input import CustomProcessInput
 from ...types import Response
 
 
 def _get_kwargs(
     process_id: str,
     *,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Dict[str, Any]:
     headers: Dict[str, Any] = {}
 
@@ -50,7 +50,7 @@ def sync_detailed(
     process_id: str,
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Response[Any]:
     """Update custom process
 
@@ -58,7 +58,7 @@ def sync_detailed(
 
     Args:
         process_id (str):
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:
@@ -86,7 +86,7 @@ async def asyncio_detailed(
     process_id: str,
     *,
     client: Client,
-    body: ProcessDetail,
+    body: CustomProcessInput,
 ) -> Response[Any]:
     """Update custom process
 
@@ -94,7 +94,7 @@ async def asyncio_detailed(
 
     Args:
         process_id (str):
-        body (ProcessDetail):
+        body (CustomProcessInput):
         client (Client): instance of the API client
 
     Raises:

{cirro_api_client-0.3.2 → cirro_api_client-1.0.0}/cirro_api_client/v1/models/__init__.py

@@ -40,6 +40,7 @@ from .create_project_access_request import CreateProjectAccessRequest
 from .create_reference_request import CreateReferenceRequest
 from .create_response import CreateResponse
 from .custom_pipeline_settings import CustomPipelineSettings
+from .custom_process_input import CustomProcessInput
 from .customer_type import CustomerType
 from .dashboard import Dashboard
 from .dashboard_dashboard_data import DashboardDashboardData
@@ -47,6 +48,8 @@ from .dashboard_info import DashboardInfo
 from .dashboard_request import DashboardRequest
 from .dashboard_request_dashboard_data import DashboardRequestDashboardData
 from .dashboard_request_info import DashboardRequestInfo
+from .data_file import DataFile
+from .data_file_metadata import DataFileMetadata
 from .dataset import Dataset
 from .dataset_assets_manifest import DatasetAssetsManifest
 from .dataset_condition import DatasetCondition
@@ -149,12 +152,12 @@ from .task import Task
 from .tenant_info import TenantInfo
 from .update_dataset_request import UpdateDatasetRequest
 from .update_user_request import UpdateUserRequest
-from .update_user_request_settings import UpdateUserRequestSettings
 from .upload_dataset_create_response import UploadDatasetCreateResponse
 from .upload_dataset_request import UploadDatasetRequest
 from .user import User
 from .user_detail import UserDetail
 from .user_project_assignment import UserProjectAssignment
+from .user_settings import UserSettings
 from .validate_file_requirements_request import ValidateFileRequirementsRequest
 
 __all__ = (
@@ -199,12 +202,15 @@ __all__ = (
     "CreateResponse",
     "CustomerType",
     "CustomPipelineSettings",
+    "CustomProcessInput",
     "Dashboard",
     "DashboardDashboardData",
     "DashboardInfo",
     "DashboardRequest",
     "DashboardRequestDashboardData",
     "DashboardRequestInfo",
+    "DataFile",
+    "DataFileMetadata",
     "Dataset",
     "DatasetAssetsManifest",
     "DatasetCondition",
@@ -307,11 +313,11 @@ __all__ = (
     "TenantInfo",
     "UpdateDatasetRequest",
     "UpdateUserRequest",
-    "UpdateUserRequestSettings",
     "UploadDatasetCreateResponse",
     "UploadDatasetRequest",
     "User",
     "UserDetail",
     "UserProjectAssignment",
+    "UserSettings",
     "ValidateFileRequirementsRequest",
 )

cirro_api_client-0.3.2/cirro_api_client/v1/models/process_detail.py → cirro_api_client-1.0.0/cirro_api_client/v1/models/custom_process_input.py

@@ -12,36 +12,35 @@ if TYPE_CHECKING:
     from ..models.pipeline_code import PipelineCode
 
 
-T = TypeVar("T", bound="ProcessDetail")
+T = TypeVar("T", bound="CustomProcessInput")
 
 
 @_attrs_define
-class ProcessDetail:
+class CustomProcessInput:
     """
     Attributes:
         id (str): Unique ID of the Process Example: process-hutch-magic_flute-1_0.
         name (str): Friendly name for the process Example: MAGeCK Flute.
-        description (str):  Example: MAGeCK Flute enables accurate identification of essential genes with their related
-            biological functions.
+        description (str): Description of the process Example: MAGeCK Flute enables accurate identification of essential
+            genes with their related biological functions.
         executor (Executor): How the workflow is executed
         child_process_ids (List[str]): IDs of pipelines that can be run downstream
-        parent_process_ids (List[str]): IDs of pipelines that can run this pipeline
-        linked_project_ids (List[str]): Projects that can run this pipeline
+        parent_process_ids (List[str]): IDs of processes that can run this pipeline
+        linked_project_ids (List[str]): Projects that can run this process
         data_type (Union[None, Unset, str]): Name of the data type this pipeline produces (if it is not defined, use the
             name)
         category (Union[Unset, str]): Category of the process Example: Microbial Analysis.
         pipeline_type (Union[Unset, str]): Type of pipeline Example: nf-core.
-        documentation_url (Union[None, Unset, str]): Link to pipeline documentation Example:
+        documentation_url (Union[None, Unset, str]): Link to process documentation Example:
             https://docs.cirro.bio/pipelines/catalog_targeted_sequencing/#crispr-screen-analysis.
         file_requirements_message (Union[None, Unset, str]): Description of the files to be uploaded (optional)
         pipeline_code (Union['PipelineCode', None, Unset]):
-        owner (Union[None, Unset, str]): Username of the pipeline creator (blank if Cirro curated)
-        is_tenant_wide (Union[Unset, bool]): Whether the pipeline is available to all projects in the organization
+        is_tenant_wide (Union[Unset, bool]): Whether the process is shared with the tenant
         allow_multiple_sources (Union[Unset, bool]): Whether the pipeline is allowed to have multiple dataset sources
+        uses_sample_sheet (Union[Unset, bool]): Whether the pipeline uses the Cirro-provided sample sheet
         custom_settings (Union['CustomPipelineSettings', None, Unset]):
-        is_archived (Union[Unset, bool]): Whether the process is marked for removal
-        file_mapping_rules (Union[List['FileMappingRule'], None, Unset]): Describes the files that this dataset type
-            expects.
+        is_archived (Union[Unset, bool]): Whether the process is marked as archived
+        file_mapping_rules (Union[List['FileMappingRule'], None, Unset]):
     """
 
     id: str
@@ -57,9 +56,9 @@ class ProcessDetail:
     documentation_url: Union[None, Unset, str] = UNSET
     file_requirements_message: Union[None, Unset, str] = UNSET
     pipeline_code: Union["PipelineCode", None, Unset] = UNSET
-    owner: Union[None, Unset, str] = UNSET
     is_tenant_wide: Union[Unset, bool] = UNSET
     allow_multiple_sources: Union[Unset, bool] = UNSET
+    uses_sample_sheet: Union[Unset, bool] = UNSET
     custom_settings: Union["CustomPipelineSettings", None, Unset] = UNSET
     is_archived: Union[Unset, bool] = UNSET
     file_mapping_rules: Union[List["FileMappingRule"], None, Unset] = UNSET
@@ -113,16 +112,12 @@ class ProcessDetail:
         else:
             pipeline_code = self.pipeline_code
 
-        owner: Union[None, Unset, str]
-        if isinstance(self.owner, Unset):
-            owner = UNSET
-        else:
-            owner = self.owner
-
         is_tenant_wide = self.is_tenant_wide
 
         allow_multiple_sources = self.allow_multiple_sources
 
+        uses_sample_sheet = self.uses_sample_sheet
+
         custom_settings: Union[Dict[str, Any], None, Unset]
         if isinstance(self.custom_settings, Unset):
             custom_settings = UNSET
@@ -170,12 +165,12 @@ class ProcessDetail:
             field_dict["fileRequirementsMessage"] = file_requirements_message
         if pipeline_code is not UNSET:
             field_dict["pipelineCode"] = pipeline_code
-        if owner is not UNSET:
-            field_dict["owner"] = owner
         if is_tenant_wide is not UNSET:
             field_dict["isTenantWide"] = is_tenant_wide
         if allow_multiple_sources is not UNSET:
             field_dict["allowMultipleSources"] = allow_multiple_sources
+        if uses_sample_sheet is not UNSET:
+            field_dict["usesSampleSheet"] = uses_sample_sheet
         if custom_settings is not UNSET:
             field_dict["customSettings"] = custom_settings
         if is_archived is not UNSET:
@@ -254,19 +249,12 @@ class ProcessDetail:
 
         pipeline_code = _parse_pipeline_code(d.pop("pipelineCode", UNSET))
 
-        def _parse_owner(data: object) -> Union[None, Unset, str]:
-            if data is None:
-                return data
-            if isinstance(data, Unset):
-                return data
-            return cast(Union[None, Unset, str], data)
-
-        owner = _parse_owner(d.pop("owner", UNSET))
-
         is_tenant_wide = d.pop("isTenantWide", UNSET)
 
         allow_multiple_sources = d.pop("allowMultipleSources", UNSET)
 
+        uses_sample_sheet = d.pop("usesSampleSheet", UNSET)
+
         def _parse_custom_settings(data: object) -> Union["CustomPipelineSettings", None, Unset]:
             if data is None:
                 return data
@@ -308,7 +296,7 @@ class ProcessDetail:
 
         file_mapping_rules = _parse_file_mapping_rules(d.pop("fileMappingRules", UNSET))
 
-        process_detail = cls(
+        custom_process_input = cls(
             id=id,
             name=name,
             description=description,
@@ -322,16 +310,16 @@ class ProcessDetail:
             documentation_url=documentation_url,
             file_requirements_message=file_requirements_message,
             pipeline_code=pipeline_code,
-            owner=owner,
             is_tenant_wide=is_tenant_wide,
             allow_multiple_sources=allow_multiple_sources,
+            uses_sample_sheet=uses_sample_sheet,
             custom_settings=custom_settings,
             is_archived=is_archived,
             file_mapping_rules=file_mapping_rules,
         )
 
-        process_detail.additional_properties = d
-        return process_detail
+        custom_process_input.additional_properties = d
+        return custom_process_input
 
     @property
     def additional_keys(self) -> List[str]: