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Add Omics functions #48
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7148742
Adding AWS Omics support
golharam 2aab385
Remove hard-coded role arn
golharam b47fad3
Remove hard-coded output path
golharam f4b1d19
Add boto3 to requirements.txt
golharam aeda697
Get role arn from connect() parameters
golharam 4107460
Add stage_output_files
golharam 7f190ab
Update get_project
golharam 3e45a6f
Revert get_project
golharam 4e5cdfa
Add notes for copy_folder
golharam f6f1dd8
Add trailing slash only if its missing
golharam e551a39
Add output_bucket
golharam 83803c4
Add output_bucket
golharam 0088068
Implement throttling to 1 TPS on Omics
golharam 01e5f6f
Implement throttling to 1 TPS on Omics
golharam 64089fe
Merge branch 'main' into add_omics
golharam eedf286
Merge branch 'main' into add_omics
golharam 2d2f654
Merge branch 'main' into add_omics
golharam 1667013
Adding unit tests for AWS Omics
golharam 406bc2b
Add missing implementations for functions
golharam 6a2099d
Add comment
golharam a74d2a2
Merge branch 'main' into add_omics_functions
maggiecbms e65a629
make omics consistent with base
maggiecbms 525ca41
add function to support launcher;
maggiecbms 5ff2af7
add s3 client to init
maggiecbms 5091fb5
Merge branch 'main' into add_omics_functions
maggiecbms 78e4f9d
update upload_file function name
maggiecbms dce5a5e
add omics function
maggiecbms d2d0950
remove space in output url
maggiecbms 8b101b4
Add TODO comments
golharam 32318d6
update storagetype for omics
maggiecbms 76bd233
Merge branch 'main' into add_omics_functions
golharam 6c54636
Create a run group for omics when calling create_project
golharam 190a78f
Return the rungroupid
golharam 1eb5a1a
Add missing get_project_cost
golharam fc4f27c
Add stubs to missing methods
golharam 7ab2228
Revert run_group_id -> projectid
golharam d2be6ea
Remove hardcoded values from omics_platform.py
golharam d12a9f9
fix output path in omics_platform.py
golharam f389323
Force failure if output_bucket and role_arn are not provided
golharam 97a76b6
add get_project_by_name for omics
maggiecbms 78e1d98
allow not finding project by name
maggiecbms ffcd06a
update get task output
maggiecbms 7219cf9
update omics formats
maggiecbms fa1b00e
add check for locations
maggiecbms 96b2fc1
add omics unit test
maggiecbms 591bf66
fix omics unit test
maggiecbms 9471af1
add cache
maggiecbms 30cd9f1
Merge remote-tracking branch 'origin/main' into add_omics_functions
maggiecbms 9620775
update omics wes api
maggiecbms bbd59d7
get api username password from environment
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,7 @@ | ||
| boto3 | ||
| chardet | ||
| smart_open | ||
| arvados-python-client>=3.0.0,<3.2.0 | ||
| sevenbridges-python | ||
| tenacity | ||
| httpx |
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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