Collecting Writeups

At the end of a typical challenge on Synapse, all participating users and teams will be asked to provide a writeup on their submission(s). The writeup should include details such as methodologies, external data sources (if any), and source code and/or Docker images. Participants and teams will submit their writeups as Synapse projects.

Although not true for all challenges, writeups are typically a criterion for any challenge incentives, such as “top performer” eligibility, byline authorship, and more.

If you are a challenge organizer and your challenge will require writeups, this article will help you:

• Set up the infrastructure for collecting and validating writeup submissions

• Display the writeups on a leaderboard

Workflow Setup

Requirements

• One Sage account

• (for local testing) CWL runner of choice, e.g. cwltool

• Access to cloud compute services, e.g. AWS, GCP, etc.

Outcome

This infrastructure will continuously monitor the writeup queue for a new submission, perform a quick validation, and, if valid, create an archive of the submission. An archive is created to ensure a copy of the writeup is always available to the organizers team, in case the project owner deletes the original copy or remove accessibility.

Steps

1. On the live project, go to the Challenge tab and check whether there is already an evaluation queue for collecting writeups (skip to Step 3 if so).

2. Create a new evaluation queue if one is not available. Click on Challenge Tools > Add Evaluation Queue, and name it something like <Challenge Name> Writeup

By default, the newly-created queue will only be accessible to the creator, in this case, you. For now, update its sharing settings so that:

• The organizers team has Can score permissions

• The admin team has Adminstrator permissions

• Anyone on the web has Can view permissions

We recommend not sharing the evaluation queue with the participants team until after the workflow has been tested.

3. Update the quota of the writeup evaluation queue, such as the Duration and Submission Limits. Generally, there are no submission limits for writeups, so this field can be left blank.

4. Go to Sage-Bionetworks-Challenges, and create a New repo.

For “Repository template”, select Sage-Bionetworks-Challenges/writeup-workflow. The “Owner” can be left as default, and give any name you’d like for “Repository name”.

Past naming examples are:

• Anti-PD1-DREAM-Writeups

• CTD2-Chemosensitivity-Writeup

• RA2-Writeup-Infrastructure

Before creating the repo, switch the view from Private to Public.

5. Clone the repo onto your machine. Using a text editor or IDE, make the following updates to workflow.cwl:

Push the changes up to GitHub when done.

6. On the staging project, go to the Files tab and click on the upload icon to Upload or Link to a File:

Open

7. In the pop-up window, switch tabs to Link to URL. For "URL", enter the web address to the zipped download of the workflow infrastructure repository.  You may get this address by going to the repository and clicking on Code > right-clicking Download Zip > Copy Link Address:

Open

Click Save.

8. Add an annotation to the file called ROOT_TEMPLATE by clicking on the annotations icon, followed by Edit:

Open

For “Value”, enter the path to the workflow script, written as:

{name of repo}-{branch}/workflow.cwl

For example: my-writeup-repo-main/workflow.cwl

9. There are two approaches for running the writeup workflow. You can either:

10. (optional but recommended for Displaying Writeups in a Leaderboard) Create a Submission View so that you can track and monitor the writeup submissions.

We recommend the following schema for monitoring writeup submissions:

Submit Dry-runs

Use and/or create a new Synapse project and submit it to the writeup queue. You can directly submit to the queue within the Challenge tab of the live project:

Open

Some cases we recommend testing for are:

Once you are satisfied that the writeup workflow is to your expectations, remember to open the queue to the challenge participants!

You can do so by updating its sharing settings so that the participants team has Can submit permissions.

Display Writeups in a Leaderboard

Once the challenge has concluded and top-performers are ready to be announced, a “Final Results” leaderboard will typically be created to include writeups alongside the final submissions and their scores. This will enable the sharing of solutions and algorithms submitted to the challenge.

Creating this leaderboard can be achieved with a Materialized View table.

Requirements

• synID of Submission View for final submissions

• synID of Submission View for writeups

• challengeutils (for syncing changes)

Steps

1. Go to the staging project and click on the Tables tab. Create a new Materialized View by clicking on Add New… > Add Materialized View.

2. Under “Defining SQL”, enter the following query:

This query will join the Submission View for submissions (s) with the Submission View for writeups (w), using the submitterids from both Views as the index. Rows are filtered to only include valid submissions from both Views (*.status = 'ACCEPTED') – these clauses are optional and can be removed if desired.

Columns selected from the submissions View (s) include:

• submission ID (s.id)

• submission date (s.createdOn)

• participant/team (s.submitterid)

• status (s.status)

• any annotations related to scores

Columns selected from the writeups View (w) include:

• synID of the writeup (w.entityid)

• synID of the writeup archive (w.archive)

The query is also assigning aliases, e.g. w.entityid AS writeup, for readability and easier querying.

3. Click Save. A table with the selected columns from each Submission View will now be available for viewing and querying.

4. Continuing on the staging project, switch to the Wiki tab and go to the “Results” page (create a new page if it’s not available). Click on the pencil icon to Edit Project Wiki:

Open

5. In the pop-up window, click on + Insert button > Table: Query on a Synapse Table/View:

Open

5. For “Query”, enter something like:

where syn123 is the synID to the MaterializedView created in Step 3. Optionally include aliases and/or clauses to the query if desired, e.g. exclude certain columns such as archived_writeup. Click on the Preview button in the top-left corner to preview the prospective leaderboard, e.g.

Open

Querying a view and assigning aliases

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Leaderboard preview

6. Click Save once you are satisfied with the final leaderboard.

7. Sync changes to the live site with challengeutils' mirror-wiki:

For additional assistance or guidance, contact the Challenges and Benchmarking team at cnb@sagebase.org.