Automating Research Data Flows with Globus (CHPC 2019 - South Africa)
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The document discusses automating research data workflows using the Globus Command Line Interface (CLI). Key points include: 1) The CLI can be used to automate recurring transfers, stage data in/out of compute jobs, and allow applications to submit transfers on a user's behalf by using access tokens. 2) Refresh tokens allow applications to get new access tokens without a user logged in, by storing and exchanging refresh tokens. 3) Examples of automation include syncing directories with scripts, staging data in shared directories, and removing directories after transfer with Python scripts. 4) Resources for support include Globus documentation, sample code, and professional services for custom application development and integration.
![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]'](https://image.slidesharecdn.com/191205chpc201904automationglobuscli-191221151458/85/Automating-Research-Data-Flows-with-Globus-CHPC-2019-South-Africa-16-320.jpg)
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Automating Research Data Flows with Globus (CHPC 2019 - South Africa)
- 1. Automating Research Data Workflows Vas Vasiliadis [email protected] CHPC National Conference December 5, 2019
- 2. Data replication/migration/distribution • For backup: initiated by user or system back up • Automated transfer of data from science instrument • Staging of reference data subset from repository 3 Recurring transfers with sync option Copy /ingest Daily @ 3:30am
- 3. Staging data with compute jobs • Stage data in or out as part of the job • Transfer task is submitted when the job is run – Endpoint may not be currently activated • Alternative approaches 1. User adds directives to job submission script 2. Application manages data staging on user’s behalf
- 4. Application driven automation • Application (e.g. portal, science gateway) submits a transfer of compute results as the user • Application monitors transfer, and initiates additional processing and/or backup of data
- 6. Globus Auth: Native apps • Client that cannot keep a secret, e.g… – Command line, desktop apps – Mobile apps – Jupyter notebooks • Native app is registered with Globus Auth – Not a confidential client • Native App Grant is used – Variation on the Authorization Code Grant • Globus SDK: – To get tokens: NativeAppAuthClient – To use tokens: AccessTokenAuthorizer 7
- 7. Browser Native App grant 8 Native App (Client) 1. Run application 2. URL to authenticate 3. Authenticate and consent 4. Auth code 5. Register auth code 6. Exchange code 7. Access tokens 8. Authenticate with access tokens to invoke transfer service as user App/Service (Resource Server) Globus Auth (Authorization Server)
- 8. Refresh tokens • Common use cases – Portal checking transfer status when user is not logged in – Running command line app from script • Refresh tokens issued to client, in particular scope • Client uses refresh token to get access token – Confidential client: client_id and client_secret required – Native app: client_secret not required • Refresh token good for 6 months after last use • Consent rescindment revokes all tokens 9
- 9. Refresh tokens 10 Native App (Client) App/Service (Resource Server) Globus Auth (Authorization Server) 1. Run application 2. URL to authenticate Browser 3. Authenticate and consent 4. Auth code 5. Register auth code 6. Exchange code, request refresh tokens 7. Access tokens and refresh tokens 9. Exchange refresh token for new access tokens 8. Store refresh tokens 10. Access tokens 11. Authenticate with access tokens to invoke service as user
- 10. 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 11 Run them on your EC2 instance in ~globus/native-app-examples
- 11. Automation via the Globus CLI
- 12. Globus Command Line Interface (CLI) • Native application: docs.globus.org/cli/installation • Open source, uses Python SDK – globus login – get access/refresh tokens (~/.globus.cfg) – globus logout – delete tokens • Service (Transfer/Auth) invocation uses tokens • Getting help: globus --help, globus list-commands docs.globus.org/cli/examples Available on your EC2 instance (log in as user “globus”)
- 13. UUIDs everywhere • UUIDs for endpoint, task, user identity, groups… • Use search/list options • get-identities for identity username to UUID $ globus endpoint search 'Globus Tutorial' $ globus task list $ globus get-identities [email protected] df191fb8-ac4d-42b6-966e-a89f07a63dc0
- 14. Batch Transfers • Transfer tasks have one source/destination, but can have any number of files • Provide input source-dest pairs via local file • e.g. move files listed in files.txt from $ep1 to $ep2 $ ep1=ddb59aef-6d04-11e5-ba46-22000b92c6ec $ ep2=ddb59af0-6d04-11e5-ba46-22000b92c6ec $ globus transfer $ep1:/share/godata/ $ep2:/~/ -- batch --label 'CLI Batch' < files.txt
- 15. Useful submission options • Safe resubmissions – Applies to all tasks (transfer and delete) – Get a task UUID and use it in submission – $ globus task generate-submission-id – Use --submission-id option in transfer command • Task wait – Useful for scripting conditional on transfer task status
- 16. 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]'
- 17. Managing notifications • Turn off emails sent for tasks • Useful when an application manages tasks for a user • Disable notifications with the --notify option --notify off (all notifications) --notify succeeded|failed|inactive (select notifications)
- 18. Permission management • Set and manage permissions on shared endpoint • Requires access manager role $ share=<shared_endpoint_UUID> $ globus endpoint permission create --permissions r -- identity [email protected] $share:/NCARTest/ $ globus endpoint permission list $share $ globus endpoint permission delete $share <perm_UUID>
- 19. Example: Recurring transfers • Submit CLI transfer(s) via task manager/cron • Useful for periodic sync, backup • Interactions are as user: both for data access and to invoke Globus services
- 20. Example: Job submission data staging • CLI installed on head node • User runs globus login; tokens stored in user’s home directory • Tokens accessible when job runs and submits stage in/out tasks • Use --skip-activation-check when submitting task – Task accepted even if endpoint is not activated at submit time – Task held until endpoint is activated
- 21. Example: Automation with portals • Portal needs to act as the user • User grants “offline” access to the portal – Portal gets and stores refresh tokens for each user – Uses client id/secret + refresh tokens to get new access tokens – Portal maintains state about transfers being managed (task id)
- 22. Automation Examples • Syncing a directory – bash script; calls the Globus CLI – Python module; run as script or import as module • Staging data in a shared directory – bash and Python variants • Removing directories after files are transferred – Python script 23 github.com/globus/automation-examples
- 23. Walkthrough • Sample script that uses sync option to transfer files github.com/globus/automation- examples/blob/master/cli-sync.sh • Same task, via an app that uses Python SDK github.com/globus/automation- examples/blob/master/globus_folder_sync.py
- 24. Support resources • Globus documentation: docs.globus.org • Sample code: github.com/globus • Helpdesk and issue escalation: [email protected] • Customer engagement team • Globus professional services team – Assist with portal/gateway/app architecture and design – Develop custom applications that leverage the Globus platform – Advise on customized deployment and integration scenarios
- 25. Join the Globus community • Access the service: globus.org/login • Create a personal endpoint: globus.org/app/endpoints/create-gcp • Documentation: docs.globus.org • Engage: globus.org/mailing-lists • Subscribe: globus.org/subscriptions • Need help? [email protected] • Follow us: @globusonline