We provide an overview of the various Globus capabilities that can be used to automate data flows, with particular emphasis on managing data from instruments such as next generation sequencers and cryo electron microscopes. This session introduces the Globus command line interface (CLI) for integrating Globus tasks into scripts, and the Globus Flows service for more robust automation (including workflows that require a human in the loop). Presented at a workshop at KU Leuven on July 8, 2022.

1. Using Globus to Streamline
Research at Scale
Vas Vasiliadis
vas@uchicago.edu
8 July 2022

2. Globus Automation Capabilities
Timer Service
Scheduled and recurring transfers
(a.k.a. Globus cron)
Command Line Interface
Ad hoc scripting and integration
Globus Flows service
Comprehensive task (data and
compute) orchestration with human in
the loop interactions

3. Three perspectives
• Researcher: ease of use, scalability
• Administrator: visibility, access control
• Builder

4. Globus Timer Service

5. Use case: Data replication
• For backup: initiated by user or system back up
• Automated transfer of data from science instrument
5
Recurring transfers
with sync option
Copy /ingest
Daily @ 3:30am

6. The Globus Timer service
• Scheduled/recurring file transfers
• Supports all Globus transfer and sync options
• Service accessible via web app and CLI
• Example: NIH – hpc.nih.gov/storage/globus_cron.html
6

7. Timer options
in the Globus
web app

8. Using the Globus Timer service
8
$ globus–timer session {login, logout, whoami}
$ globus–timer job transfer
--name example–job
--label "Timer Transfer Job"
--interval 28800
--start '2020–01–01T12:34:56'
--source–endpoint ddb59aef–6d04–11e5–ba46–22000b92c6ec
--dest–endpoint ddb59af0–6d04–11e5–ba46–22000b92c6ec
--item ~/file1.txt ~/new_file1.txt false
--item ~/file2.txt ~/new_file2.txt false

9. Scheduled transfers
using Globus
timers
9

10. Globus Command Line
Interface (CLI)

11. Globus Command Line Interface
Open source, uses
the Python SDK

12. UUIDs everywhere
• UUIDs for endpoint, task, user identity, groups…
• Use search/list options
• get-identities for identity username to UUID
$ globus endpoint search 'Tutorial Endpoint 1'
$ globus task list
$ globus get-identities vas@globusid.org
bfc122a3-af43-43e1-8a41-d36f28a2bc0a

13. Step 1: Transfer files
$ export src=<source_collection_UUID>
$ export dst=<destination_collection_UUID>
$ globus transfer --recursive $src:/~/carousel
$dst:/globusworkshop
$ globus task show <transfer_task_UUID>

14. Step 2: Set permissions
• Set and manage permissions on guest collection
• Requires access manager role
$ export share=<guest_collection_UUID>
$ globus endpoint permission create --permissions r --
identity demodoc@globusid.org $share:/globusworkshop/
$ globus endpoint permission list $share
$ globus endpoint permission delete $share <perm_UUID>

15. Parsing CLI output
• Default output is text; for JSON output use --format json
$ globus endpoint search --filter-scope my-endpoints
$ globus endpoint search --filter-scope my-endpoints --
format json
• Extract specific attributes using --jmespath <expression>
$ globus endpoint search --filter-scope my-endpoints --
jmespath 'DATA[].[id, display_name]'

16. Using the CLI for automation requires…
• Evergreen auth à native app grant w/refresh tokens
• Guest collections
• Delegated permissions management

17. Globus Auth: Native apps
• Client that cannot keep a secret: CLI, mobile, Jupyter
notebooks, …
• Register with Globus Auth à special callback URL
• Native App grant is variation on the Authorization
Code grant
20

18. Native App/Refresh Tokens Sample Code
github.com/globus/native-app-examples
• ./example_copy_paste.py
– User copies and pastes code to the app
• ./example_copy_paste_refresh_token.py
– Stores refresh token locally, uses it to get new access tokens
• See README for installation
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19. Automation services ecosystem
GET /provider_url/
POST /provider_url/run
GET /provider_url/action_id/status
GET /provider_url/action_id/cancel
GET /provider_url/action_id/status
Create Action
Providers
Define and
deploy flows
{ “StartAt”: ”ToProject”,
”States” : {
”ToProject” : { … },
”SetPermission” : { …},
“ProcessData” : { … } … }}
Run flows

20. Globus Flows Service

21. Managed automation of tasks
• Flows: A platform service for defining, applying, and
sharing distributed research automation flows
• Flows comprise Actions
• Action Providers: Called by Flows to perform tasks
• Triggers*: Start flows based on events
* In development

22. Automation with Globus Flows
• Built on AWS Step Functions
– Simple JSON-based state machine
language
– Conditions, loops, fault tolerance, etc.
– Propagates state through the flow
• Standardized API for integrating
custom event and action services
– Actions: synchronous or asynchronous
– Custom Web forms prompt for user input
• Actions secured with Globus Auth

23. 26
Run flows: Guided input
Label
Notify user
Timeout
Dynamic forms generated
from input schema

24. 27
Managing runs at scale

25. Globus-provided flows
28

26. Running a
Globus Flow
29

27. Developing
Globus Flows
jupyter.demo.globus.org
30

28. Extending the ecosystem: Action providers
31
• Action Provider is a
service endpoint
– Run
– Status
– Cancel
– Release
– Resume
• Action Provider Toolkit
action-provider-
tools.readthedocs.io/en/latest
Search
Transfer
Notification
ACLs Identifier
Delete
Ingest
User
Form
Describe Xtract
funcX Web
Form
Custom built
Globus Provided