HTAN2 Synapse Project Setup

Note

These scripts are intended for internal use by the HTAN DCC.
Resulting projects will not be publically accessible

create_project.py

This script automates the creation of projects in Synapse and sets permissions for specific teams. If a project already exists, it resets the permissions for that project. After execution, the script saves the created or updated project names and their corresponding Synapse IDs in a projects.yml file.

Features

• Automatically creates Synapse projects if they do not exist.
• Resets permissions for existing Synapse projects.
• Adds specified teams to the projects with customizable permissions.
• Saves the project names and Synapse IDs to projects.yml.

Prerequisites

• Python 3.x
• Synapse Python Client (synapseclient)
• PyYAML (yaml for reading/writing YAML files)

Install dependencies

You can install the necessary Python libraries with the following command:

pip install synapseclient pyyaml

Usage

1. Clone the repository or copy the script to your local machine.

2. Open the script and make sure the following fields are correct:

   • project_names: A list of project names that you want to create or manage in Synapse.
   • htan_dcc_admins_team_id: The ID of the HTAN DCC Admins team.
   • htan_dcc_team_id: The ID of the HTAN DCC team.
   • act_team_id: The ID of the ACT team.

3. Run the script using Python:

python synapse_project_creator.py

4. The script will:
   • Log into Synapse.
   • Loop through the project names.
   • Create the project if it doesn't exist or reset its permissions if it already exists.
   • Set team permissions for the projects.
   • Save the project name and Synapse ID to projects.yml.

Output of projects.yml

After running the script, the projects.yml file will contain project names and their corresponding Synapse IDs. This is presented as a table below

Project	Synapse ID
HTAN2	syn63296487
HTAN2_Ovarian	syn63298044
HTAN2_Glioma	syn63298048
HTAN2_Gastric	syn63298051
HTAN2_Skin	syn63298054
HTAN2_Pediatric	syn63298059
HTAN2_Myeloma	syn63298063
HTAN2_Pancreatic	syn63298065
HTAN2_Prostate	syn63298068
HTAN2_CRC	syn63298073
HTAN2_Lymphoma	syn63298076

Customization

• Project Names: You can modify the project_names list to include any project names you need.
• Permissions: The permissions for each team can be adjusted within the set_project_permissions function.
  • The current setup adds admin permissions to the HTAN DCC Admins and ACT teams, while the HTAN DCC team gets edit and delete permissions.

Troubleshooting

• If you encounter a SynapseHTTPError, ensure that your Synapse credentials are correct and you have the necessary permissions to create and manage the projects.
• Verify that the team IDs are accurate by checking the Synapse web interface.