Supervisors (assignee) section

Your task as the PR Assignee is to supervise the reviewing process, controlling that the steps are taken in the established way and providing moderation or giving a second opinion if needed.

The following is the order of events that should happen during the process:

1. After finishing the curation, a Researcher will produce the EAR pdf and open a Pull Request in the ERGA-consortium/EARs repo to get the assembly reviewed. The description (body) of the PR should have a message starting with "Assembly review request" and providing ToLID, Species, Project and Affiliation.

2. When the PR is open, the EAR-bot will check the PR, add a tag based on the ERGA project and call a Supervisor (in the PR terminology, assignee). The messages should be:

Hi @{Researcher_GithubID}, thanks for sending the EAR of {Species}.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

Hi @{Assignee_GithubID}, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledgement.

If the EAR-bot detects any error in the PR before calling the Supervisor, it will flag the PR and ask the Researcher for a fix. The Pull Requests that are Error-flagged at this point will be monitored and handled by the repo admin.

3. If all checks are passed, you (the Supervisor) will receive a notification to go to the Pull Request (PR) because the Bot mentioned your GithubID. Your first task is to quickly double-check that the Pull Request looks correct:

• check that the project tag was added
• check that the PR comes from a separate branch (not the main branch), the submitters are asked to call this something like mHomSap1-EAR
• check that the Assembly review request description looks ok (the four fields are correctly completed)
• check that the folder structure looks ok: click the files changed tab to see the path. It should be Assembly_Reports/{Species_name}/{ToLID}/{ToLID}_EAR.pdf
• check that there is only one file that the PR is trying to merge (one species per PR is the rule for being able to isolate one species/EAR per PR), there are no conflicting commits, and that the merge is to ERGA-consortium:main
• check that the PDF looks OK and that the link for the contact map file is reachable (you need to download the PDF for that, the link can't be accessed with GitHub's PDF viewer)

If everything looks ok, reply to the bot comment with a simple "ok". This is the confirmation action that the EAR-bot is waiting to continue with the process.

If something is not right regarding those aspects, reply what is wrong so the Researcher can fix it. Anything else than "Ok" will trigger an Error-flag by the bot. And the process will be stalled until you reply "Ok".

4. With your confirmation action (the "Ok"), you are giving the good-to-go to the Bot to call the reviewer to check the EAR. Remember, you are not the reviewer of the assembly, you are the reviewer of the process, the supervisor.

5. The EAR-bot will call a reviewer to start the reviewing process. If all goes OK during the review, you will be called again to merge the PR when the review is over. The message from the Bot should be:

Thanks @{Reviewer_GithubID} for the review.
I will add a new reviewed species for you to the table when @{Assignee_GithubID} merges the PR ;)

Congrats on the assembly @{Researcher_GithubID}!
Please make sure that the fasta file to upload to ENA is generated based on the final reviewed version of the assembly. 

After @{Assignee_GithubID} confirmation, you can start with the assembly submission to save time.
The PR will be merged only when the final version of the EAR pdf is available.

6. You (the Supervisor) will receive a notification to go to the Pull Request because the bot mentioned your GithubID. At that moment, you will check that everything is OK in the process (same checks from the beginning again) and leave a final message.

It may happen that you will interact a little more during the process, not only at the beginning and the end. It is expected that throughout the review you will have a quick look at the pretext maps to help the reviewer or give a confirmation about some comments.

7. After leaving the final message, having the reviewer's approval, and everything else in order, merge the PR to end the reviewing process.

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Issues: The bot should identify issues and add the ERROR! red tag to the PR to increase awareness. If the supervisor was already assigned to that PR, the bot will call the supervisor to help handle the particular issue.

Special case. If the Researcher closes prematurely the PR, the bot will add the ERROR! tag and call you:

Attention @{Supervisor}!
The PR has been closed, but the reviewers will retain their busy status in case it is re-opened.
If the PR is going to remain closed, please instruct me to clear the active tasks.

You should try to understand what's going on by asking the Researcher. If things can get sorted out and the Researcher re-opens the PR, then the bot will call you again:

Attention @{Supervisor}!
The PR has been re-opened. Please check that everything looks OK.

Please take a look to see if everything looks right, and if so, remove the ERROR! tag.

If you check with the Researcher and the PR is going to remain closed, you (the Supervisor) must write @erga-ear-bot CLEAR to get all the reviewers in that PR released from their duties and all the tags in the PR cleared.

Please remember that you are responsible for the reviewing process of this species. Both the researcher and the reviewer will contact you (by dropping a message in the PR) for any issue. Be kind and remember that, like in every other working space, we follow the ERGA Code of Conduct during the reviewing process.