Reports

Reports

The OmixAtlas class contains functions which will enable users to generate reports, link reports to a dataset in OmixAtlas and fetch reports linked with dataset in an OmixAtlas.

Parameters:

Name	Type	Description	Default
token	str	token copy from polly.	required

Usage

from polly.OmixAtlas import OmixAtlas

omixatlas = OmixAtlas(token)

delete_linked_report(repo_key, dataset_id, report_id)

Delete the link of the report in workspaces with the specified dataset in OmixAtlas. On success displays a success message.

Parameters:

Name	Type	Description	Default
repo_key	str	repo_key(repo_name/repo_id) of the repository which is linked.	required
Dataset_id	str	dataset_id of the dataset to be unlinked	required
Report_id	str	report id associated with the report in workspaces that is to be deleted. This id can be found when invoking the fetch_linked_report() function.	required

Raises:

Type	Description
InvalidParameterException	Invalid parameter passed

Returns:

Type	Description
None	None

fetch_linked_reports(repo_key, dataset_id)

Fetch linked reports for a dataset_id in an omixatlas.

Parameters:

Name	Type	Description	Default
repo_key	str	repo_key(repo_name/repo_id) of the repository for which to fetch the report	required
Dataset_id	str	dataset_id of the dataset which to fetch the reports.	required

Raises:

Type	Description
InvalidParameterException	invalid parameters
RequestException	api request exception
UnauthorizedException	unauthorized to perform this action

Returns:

Type	Description
pd.DataFrame	A Dataframe with the details of the linked reports - who added the report, when it was added and the link.

generate_report(repo_key, dataset_id, workspace_id, workspace_path='')

This function is used to generate a metadata distribution report for a dataset belonging to the geo repository. The generated report is then saved to the workspace provided. This is a MVP release to minimise time taken by users to determine relevance of a dataset in their research, we’re enabling auto-generation of reports. These reports will contain dataset and sample level metadata along with some graphs showing how the samples are distributed. It will help them figure out which cohorts could be of interest in a given dataset. This template can be modified and we’re open to user’s feedback. This report is available on the user’s local path as well as an option to upload the report to workspaces is given.

Parameters:

Name	Type	Description	Default
repo_key	str	repo_key(repo_name/repo_id) for which the report is to be generated	required
Dataset_id	str	dataset_id for which the report is to be generated	required
Workspace_id	str	workspace_id to where the report is to be uploaded	required
workspace_path	str	workspace_path to which the report is to be uploaded	''

Raises:

Type	Description
InvalidParameterException	Empty or Invalid Parameters
UnsupportedRepositoryException	repo other than GEO/ Unsupported repo
UnauthorizedException	unauthorized to perform this task

link_report(repo_key, dataset_id, workspace_id, workspace_path, access_key)

This function is used to link a file (html or pdf) present in a workspace with the specified dataset in OmixAtlas.
On success it displays the access key URL and a success message. Org admins can now link a report present in a workspace with the specified datasets in an OmixAtlas. Once a report is linked to a dataset in OmixAtlas, it can be fetched both from front-end and polly-python.

Parameters:

Name	Type	Description	Default
repo_key	str	repo_name/repo_id of the repository to be linked	required
dataset_id	str	dataset_id of the dataset to be linked	required
workspace_id	str	workspace_id for the file which is to be linked	required
workspace_path	str	workspace_path for the file which is to be linked	required
access_key	str	access_key (private or public) depending upon the link access type to be generated.	required

Raises:

Type	Description
InvalidParameterException	invalid parameters

Returns:

Type	Description
None	None

Examples