Reports

OmixAtlas class enables users to interact with functional properties of the omixatlas such as create and update an Omixatlas, get summary of it's contents, add, insert, update the schema, add, update or delete datasets, query metadata, download data, save data to workspace etc. Args: token (str): token copy from polly. 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_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_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
`DataFrame`	A Dataframe with the details of the linked reports - who added the report, when it was added and the link.

`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. A message will be displayed on the status of the operation.

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. If public, then anyone with a Polly account with the link will be able to see the report. If private, only individuals who have access to the workspace where reports is stored will be able to see them.	required

Raises:

Type	Description
`InvalidParameterException`	invalid parameters

Returns:

Type	Description
`None`	None

`link_report_url(repo_key, dataset_id, url_to_be_linked)`

This function is used to link a URL with the specified dataset in OmixAtlas. A message will be displayed on the status of the operation.

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
`url_to_be_linked`	`str`	The url which is to be linked	required

Raises:

Type	Description
`InvalidParameterException`	invalid parameters

Returns:

Type	Description
`None`	None

Examples

# Install polly python
pip install polly-python

# Import libraries
from polly.auth import Polly
from polly.omixatlas import OmixAtlas

# Create omixatlas object and authenticate
AUTH_TOKEN=(os.environ['POLLY_REFRESH_TOKEN'])
Polly.auth(AUTH_TOKEN)
omixatlas = OmixAtlas()

Link html/pdf/json with a dataset

This function links a given report present in a workspace to the dataset_id of the given OmixAtlas.

repo_key = "geo"
dataset_id = "GSE100000_GPL17021"
workspace_id = 8108 # workspace_id as an integer
workspace_path = "GSE100000_GPL17021_report.html"
access_key = "private" # access can be made public if required, access_key="public"
omixatlas.link_report(repo_key, dataset_id, workspace_id, workspace_path, access_key)

File Successfully linked to dataset id = GSE100000_GPL17021. The URL for the private access is 'https://polly.elucidata.io/manage/restricted/file?id=8108&path=%2Fprojects%2F8108%2Ffiles%2FGSE100000_GPL17021_report.html'

Link URL with a dataset

This function is used to link a URL with the specified dataset in OmixAtlas. It must be a secure link i.e https://abc.com

repo_key = "geo"
dataset_id = "GSE100000_GPL17021"
url_to_be_linked = "'https://polly.elucidata.io/manage/restricted/file?id=8108&path=%2Fprojects%2F8108%2Ffiles%2FGSE100000_GPL17021_report.html'"
link_report_url(repo_key, dataset_id, url_to_be_linked)

Fetch reports linked with a dataset

This function is used to list of reports linked with the given dataset.

repo_key = "geo"
dataset_id = "GSE100000_GPL17021"
reports_dataframe = omixatlas.fetch_linked_reports(repo_key, dataset_id)
reports_dataframe

	Added_by	Added_time	URL	Report_id
0	vivek.mathpal@elucidata.io	17/02/2023 06:09:21	https://polly.elucidata.io/manage/restricted/f...	6aea293d-b30b-45bd-af0f-d83dcaa88b64

Delete linked reports

This function is used to delete a particular report linked to the respective dataset.

repo_key = "geo"
dataset_id = "GSE100000_GPL17021"
report_id = "6aea293d-b30b-45bd-af0f-d83dcaa88b64"
omixatlas.delete_linked_report(repo_key, dataset_id, report_id)

Linked file with report_id = '6aea293d-b30b-45bd-af0f-d83dcaa88b64' deleted.