odm_api.ManageDataApi¶

All URIs are relative to http://localhost

Method	HTTP request	Description
delete_data	DELETE /api/v1/manage-data/data	Delete objects from ODM
get_detached_objects	GET /api/v1/manage-data/detached-objects	Retrieve a list of detached objects

delete_data¶

List[ManagedObject] delete_data(accessions=accessions)

Delete objects from ODM

The objects will be marked for deletion. In case the selected object has more than one version, the endpoint deletes all of them. The following object types can be deleted by the endpoint: * STUDY * SAMPLE_GROUP * SAMPLE_OBJECT * LIBRARY_GROUP * PREPARATION_GROUP * CELL_GROUP * TABULAR_DATA * GENE_VARIANT * FLOW_CYTOMETRY * REFERENCE_GENOME * FILE

Moreover, if the selected object is linked to any other data, the endpoint will also delete the linked data associated with it according to the specified rules: * If you delete a STUDY, the entire study with all the listed group types and files, will be removed. * Deleting a SAMPLE_GROUP will result in the removal of all samples associated with this sample group, along with any linked TABULAR_DATA/GENE_VARIANT/FLOW_CYTOMETRY/LIBRARY_GROUP/PREPARATION_GROUP/CELL_GROUP. The linked TABULAR_DATA/GENE_VARIANT/FLOW_CYTOMETRY/CELL_GROUP will be deleted, even if it is linked to another metadata group. * Deleting a SAMPLE_OBJECT will result in the removal of that sample from the study, and it will not be displayed in the version history. If a LIBRARY_OBJECT or PREPARATION_OBJECT is linked to this SAMPLE_OBJECT, it will be deleted as well. * Deleting a LIBRARY_GROUP or PREPARATION_GROUP will result in the removal of all libraries or preparations associated with this group, along with any linked TABULAR_DATA/CELL_GROUP. * Deleting a CELL_GROUP will result in the removal of linked TABULAR_DATA (cell expression group). * If you delete TABULAR_DATA/GENE_VARIANT/FLOW_CYTOMETRY, all associated data, such as links and runs will be removed from ODM. * If you delete REFERENCE_GENOME, searching for variant by variantFeature (genes) won't be available for linked VCF groups. * If you delete FILE, the file will be removed from ODM.

Example¶

Api Key Authentication (Access-token):
Api Key Authentication (Genestack-API-Token):

import odm_api
from odm_api.models.managed_object import ManagedObject
from odm_api.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to http://localhost
# See configuration.py for a list of all supported configuration parameters.
configuration = odm_api.Configuration(
    host = "http://localhost"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: Access-token
configuration.api_key['Access-token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Access-token'] = 'Bearer'

# Configure API key authorization: Genestack-API-Token
configuration.api_key['Genestack-API-Token'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['Genestack-API-Token'] = 'Bearer'

# Enter a context with an instance of the API client
with odm_api.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = odm_api.ManageDataApi(api_client)
    accessions = ['accessions_example'] # List[str] | Accessions files to be deleted. (optional)

    try:
        # Delete objects from ODM
        api_response = api_instance.delete_data(accessions=accessions)
        print("The response of ManageDataApi->delete_data:\n")
        pprint(api_response)
    except Exception as e:
        print("Exception when calling ManageDataApi->delete_data: %s\n" % e)

Parameters¶

Name	Type	Description	Notes
accessions	List[str]	Accessions files to be deleted.	[optional]

Return type¶

List[ManagedObject]

Authorization¶

Access-token, Genestack-API-Token

HTTP request headers¶

Content-Type: Not defined
Accept: application/json

HTTP response details¶

Status code	Description	Response headers
202	The deletion of the following files and all linked data has started.	-
400	Deletion could not be performed due to Bad Request.	-
401	User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token]) or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI Profile page).	-
403	Not enough permissions to call method or the file is not meant to be deleted.	-
404	Some of the provided accessions could not be found in ODM. Deletion will not be preformed. Please review your list and repeat the attempt.	-
406	Some of the provided accessions do not belong to the supported object types. Deletion will not be performed. Please review your list and repeat the attempt.	-
500	An internal server error occurred. This indicates an unexpected failure in the Genestack system, please file a bug report to support@genestack.com, including the error details.	-

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get_detached_objects¶

DetachedCollection get_detached_objects(detached_object_type=detached_object_type, limit=limit, cursor=cursor)

Retrieve a list of detached objects

Retrieve various types of detached data objects. An object is defined as 'detached' if it lacks any direct or indirect link to a root-level object, which in this context is referred to as 'study'. Study is considered as detached object itself in case there are no links to objects at a lower level. Data with specific detachedObjectType can be retrieved by specifying the types in detachedObjectType parameter. The detached objects are sorted according to their detachedObjectType and genestack:accession. Specific ordering can be observed in the list of supported detached types found below. Pagination of the results can be conveniently managed using the cursor and limit parameters. Supported types of detached objects (listed in the order of retrieval) include: * STUDY * SAMPLE_GROUP * LIBRARY_GROUP * PREPARATION_GROUP * CELL_GROUP * TABULAR_DATA * GENE_VARIANT * FLOW_CYTOMETRY