Sensitive Data Submission
ECRIN Covid Repository Guide
Introduction
The goal of this guide is to guide persons in the usage of the TSD, part of the EOSC-Life Covid repository developed together with ECRIN. The repository can be found at https://covid-19-repo.usit.uio.no.
First Steps
To use this repository, the user must have already registered a dataset in ECRIN RMS Site. Once registered the user can connect to the TSD Website. The user must be in possession of a valid Life Science ID info here.
Website Login
Once the user logs in the repository, the following process: 1) the user project status is determined; 2) the user access rights are retrieved from the RMS; 3) the user is allowed to upload datasets to TSD.
Portal User as Applicant
On first interaction the user status is set to applicant. A person is created automatically in the TSD identity management system. The person is added to the applications group of the repository project pxx-applications-group. The application stats does not preclude the user with the following interaction with the site.
Portal User as TSD User
After the user application is approved, the user will obtain a TSD user pxx-<username>, becoming a full member of the project. The user must organize a video meeting with a project admin in order to obtain TSD credentials for their account (password, otp). The members of the project can have the basic access to the the TSD infrastructure and the resources of the TSD project that hosts the repository. Further information for TSD uses can be found in the TSD user guide.
Uploading Datasets
Uploading datasets/instance is done on the main portal. The uploading of dataset does not require a TSD user. The uploading of a dataset is done using the standard TSD Data Portal.
Repository Storage Structure
The repository storage structure is a directory on the durable partition of the project. It has the following structure:
where <study> is the study id Ecrin RMS, <dataset> is a dataset id, and <instanceX> is a instance id. The access to the dataset directory is given to all people that have read or write access to the dataset according to the Ecrin RMS. The users with read access only can not modify files in the directories. The access is restricted using groups pxx-r<dataset>-group (read group) and pxx-w<dataset>-group (write group). The membership of this group is updated automatically on the user login ini the covid repository.
Repository Export
To export data from the TSD project is done via the standard TSD export functionality. The export privilege can be granted to a user after confirmation from project administrator.
Last updated