Add Omics functions

[maggiecbms]

This PR includes changes to add Omics support.

[golharam]

I'm okay with merging this in. There are a couple of TODOs in the code but it seems to be working okay.

[golharam]

I think this PR is almost ready to go. The one thing I don't like is that launchers can be run with the '--project_name' field, but when submitting tasks, a 'project_id' aka run group id is expected so there is still a little discrepancy that needs to be addressed.

[golharam]

The last thing I notice is there are references to 'Output', and 'output'. Additionally files are uploaded to /outputs/jobid/inputs/....
It's a little confusing. For instance, upload_file, the target_path is "Outputs/[run_group_id]/launcher_inputs/[filename]"

Maybe we shouldn't use "Outputs" as a folder name as 'output' is used by omics for the workflow outputs.

[maggiecbms]

I think this PR is almost ready to go. The one thing I don't like is that launchers can be run with the '--project_name' field, but when submitting tasks, a 'project_id' aka run group id is expected so there is still a little discrepancy that needs to be addressed.

Unlike SBG and Arvaods, Omics allows two projects (run groups) to have identical names, so the get_project_by_name() function may find multiple run group IDs. I think using project ID would be better than using project name when using Omics.

I can work on get_project_by_name() to return the first element, so that launcher can run. But it does have a potential issue when another run group exists.

[maggiecbms]

The last thing I notice is there are references to 'Output', and 'output'. Additionally files are uploaded to /outputs/jobid/inputs/.... It's a little confusing. For instance, upload_file, the target_path is "Outputs/[run_group_id]/launcher_inputs/[filename]"

Maybe we shouldn't use "Outputs" as a folder name as 'output' is used by omics for the workflow outputs.

Currently output files of a run goes into s3://{Bucket}/Outputs/{RunGroupID}/{WorkflowID}/{TaskName}/{RunID}/ , and the upload_file() uploads files into s3://{Bucket}/Outputs/{RunGroupID}/launcher_inputs/ .

I can change the output folder to s3://{Bucket}/Project/{RunGroupID}/{WorkflowID}/{TaskName}/{RunID}/ and upload file to s3://{Bucket}/Project/{RunGroupID}/launcher_inputs/ .

[golharam]

This should return a dict where { 'runGroupId': XYZ }
?

[golharam]

This looks good:

1. Change references to ProjectId to runGroupId to remove any confusion of terms
2. Ask Claude 3.7 to implement unit tests

After that, we are good.

[maggiecbms]

This looks good:

1. Change references to ProjectId to runGroupId to remove any confusion of terms
2. Ask Claude 3.7 to implement unit tests

After that, we are good.

I have replaced the ProjectId to RunGroupId in omics_platform.py.
Unit test is also added with help of Claude.

[golharam]

Can we change the name from 'Omics' to 'AWSHealthOmics' to better reflect the real name? I think 'Omics' was just easier to say and type

[golharam]

Make this WES_API_ENDPOINT