Download as PDF, PPTX
![Data ingest with Globus Search
28
Search
Index
POST /index/{index_id}/ingest'
Search
{
"ingest_type": "GMetaList",
"ingest_data": {
"gmeta": [
{
"id": "filetype",
"subject”: "https://search.api.globus.org/abc.txt",
"visible_to": ["public"],
"content": {
"metadata-schema/file#type": "file”
}
},
...
]
}](https://image.slidesharecdn.com/211013gwtouraps05searchflows-211014032314/85/Instrument-Data-Orchestration-with-Globus-Search-and-Flows-28-320.jpg)
![Data ingest with Globus Search
29
Search
Index
POST /index/{index_id}/ingest'
Search
{
"ingest_type": "GMetaList",
"ingest_data": {
"gmeta": [
{
"id": ”weight",
"subject": "https://search.api.globus.org/abc.txt",
"visible_to": ["urn:globus:auth:identity:46bd0f56-
e24f-11e5-a510-131bef46955c"],
"content": {
"metadata-schema/file#size": ”37.6",
"metadata-schema/file#size_human": ”<50lb”
}
},
...
]
}
Visibility limited to Globus Auth identity
- Single user
- Globus Group
- Registered client application](https://image.slidesharecdn.com/211013gwtouraps05searchflows-211014032314/85/Instrument-Data-Orchestration-with-Globus-Search-and-Flows-29-320.jpg)
![Data discovery with Globus Search
30
{
"@datatype": "GSearchResult",
"@version": "2017-09-01",
"count": 1,
"gmeta": [
{
"@datatype": "GMetaResult",
"@version": "2019-08-27",
"entries": [
{ ... }
],
"subject": "https://..."
}
],
"offset": 0,
"total": 1
}
GET /index/{index_id}/search?q=type%3Ahdf5
Search
Index
Simple query
Search](https://image.slidesharecdn.com/211013gwtouraps05searchflows-211014032314/85/Instrument-Data-Orchestration-with-Globus-Search-and-Flows-30-320.jpg)
![Data discovery with Globus Search
31
POST /index/{index_id}/search
Search
Index
Complex query
{
"filters": [
{
"type": "range",
"field_name": ”pubdate",
"values": [
{
"from": "*",
"to": "2020-12-31"
}
]
}
],
"facets": [
{
"name": "Publication Date",
"field_name": "pubdate",
...
}
]
}
Search](https://image.slidesharecdn.com/211013gwtouraps05searchflows-211014032314/85/Instrument-Data-Orchestration-with-Globus-Search-and-Flows-31-320.jpg)
Uploaded byGlobus
Instrument Data Orchestration with Globus Search and Flows
This document discusses various Globus services for instrument data orchestration including the Timer service, platform services, authentication, search, transfer, flows, and the upcoming Trigger service. The Timer service allows for scheduled and recurring transfers. Platform services provide comprehensive data and compute orchestration. Authentication is handled by Globus Auth. Search allows for data description and discovery. Transfer shares and moves data. Flows automate distributed research tasks. Triggers will start flows based on events.
More Related Content
Similar to Instrument Data Orchestration with Globus Search and Flows
Instrument Data Orchestration with Globus Search and Flows
- 1. Instrument data orchestrationwith Globus Search and Flows Vas Vasiliadis vas@uchicago.edu October 13, 2021
- 2. Why we’re allhere this week… 2
- 3. Distribution Store Data Portal AdvancedComputing Facility Instrument Facility Instrument data orchestration: A common design pattern Image Analysis 3 Search/Discovery 5 Science! 6 Imaging 1 Acquisition 2 Description/Identification 4 v
- 4. Three Degrees ofAutomation Timer Service Scheduled and recurring transfers (a.k.a. Globus cron) Command Line Interface Ad hoc scripting and integration Platform Services Comprehensive data—and compute—orchestration (with human in the loop) Search Flows Transfer & Sharing
- 5. Globus Command Line Interface(CLI) …you’re all experts on this already!
- 6.
- 7. The Globus Timerservice • Scheduled/recurring file transfers • Well suited to backup/sync tasks • Service with a command line interface – Simple installation: pypi.org/project/globus-timer-cli – One-time authentication with a user identity • Example: NIH – hpc.nih.gov/storage/globus_cron.html 7
- 8. Use case: Datareplication • For backup: initiated by user or system back up • Automated transfer of data from science instrument 8 Recurring transfers with sync option Copy /ingest Daily @ 3:30am
- 9. Using the GlobusTimer service 9 $ 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
- 10. Globus Timer serviceoptions • ––items–file {file_name} • ––stop–after–runs • ––stop–after–date • Transfer behavior (equivalent to options in web app) ––sync–level (how timer behaves if files exist) ––verify–checksum ––encrypt–data ––preserve–timestamp 10
- 11. Timer options inthe webapp Coming soon….
- 12.
- 13. Relevant Globus platformcapabilities • Data transfer and sharing • Data description and discovery • Data (and compute) orchestration • Authentication and Authorization 13 Auth Search Transfer Groups Flows
- 14. Globus Auth: FoundationalIAM service Brokers authentication and authorization among… – End-users – Identity providers: enterprise, external (federated identities) – Services: resource servers with REST APIs – Apps: web, mobile, desktop, command line clients – Services acting as clients to other services • OAuth 2.0 Authorization Framework (a.k.a. OAuth2) • OpenID Connect Core 1.0 (a.k.a. OIDC) Auth 14
- 15. Several authentication modelssupported • Application acting as user with consent – Authorization code grant • Application authenticating as itself – Client credentials grant • Application able to manage tokens for offline or long running tasks – Refresh tokens
- 16. Authorization Code Grant 16 Client (WebPortal, Application) Globus service (Resource Server) Globus Auth (Authorization Server) 5. Authenticate using client id and secret, send authorization code Browser (User) 1. Access portal 2. Redirect user 3. User authenticates and consents 4. Authorization code 6. Access token(s) 7. Authenticate with access token(s), giving client authority to invoke the requested service Identity Provider
- 17. Client credential grant 17 1.Authenticate with app client id and secret 2. Access Tokens Application, Science Gateway, Data Portal (Client) 3. Authenticate as app with access tokens to invoke service (on behalf of authorized user, within a given scope) Globus Transfer (Resource Server) Globus Auth (Authorization Server)
- 18. Step 0: Applicationregistration • Set desired scopes • Set callback URL • Get client ID and secret • Consents implement least privileges principle 18 Auth developers.globus.org
- 19. Data transfer andsharing …you already know how to do this ;-) • Move data to collection à Submit Transfer task • Make data accessible à Set guest collection access rule • Grant user/app access à Add/confirm Group membership 19 Groups service Transfer service GET /groups/my_groups POST /endpoint/{endpoint_id}/access POST /transfer Groups Transfer
- 20. Using guest collectionsin your apps • Create a guest collection; requires authentication – Cannot be completely automated – must ”log in” – Create once and automate rest of the steps • Grant the application Access Manager role – Allows the application to manage permissions on the collection – Set for application identity: appclientid@clients.auth.globus.org • Grant roles for management of endpoint and tasks Transfer
- 21.
- 22. Data description anddiscovery • Metadata store with fine- grained visibility controls • Schema agnostic à dynamic schemas • Simple search using URL query parameters • Complex search using search request document 22 docs.globus.org/api/search Search Index Search
- 23. Cancer Registry Recordsfor Research (CR3) • Create network of federated cancer registries – Deploy similar infrastructure at other cancer registries – Enable queries across multiple registries • Federation via Globus: network scale ßà local control – Data owners input/export data sets, apply QC, set access policies – Registry data remain at the institution where they were generated – Identities are provided/authenticated by the institution, not Globus – System scale depends on data owners providing storage resources
- 24. CR3 Discovery Portal Cohort aggregate counts Login with UPMC/Pitt credentials Globus Search (GS) Globus Auth(GA) UPMC/Pitt Identity Providers Authentication Auth initiated to GA Cohort search initiated to GS Researcher Cohort aggregate counts returned CR3 Architecture Globus Transfer (GT) Registry Staff Data transfer from registrar to researcher mediated by GT Manage authorization Elasticsearch Request Service Cancer Registry De-identified Data Index (minimal criteria data: e.g., staging)
- 25. CR3 requirements • SearchIndex – Only de-identified data in search index – No record-level for researchers • Portal – Fine-grained access control – Researchers must use a specific identity – Access must be logged – Render graphs based on search results – Faceted search in real time
- 26. CR3 Portal (simulateddata) Federated logon using Globus Auth with Pitt/UPMC as identity providers Dynamically updating charts as facets change Variable facets based on source registry index Google-like text search with facets for filtering Developed using a framework based on the Globus Modern Research Data Portal* design pattern (docs.globus.org/mrdp) * PeerJ Articles:cs-144 https://peerj.com/articles/cs-144/
- 27. Distinct access policies maybe applied to Data and Metadata
- 28. Data ingest withGlobus Search 28 Search Index POST /index/{index_id}/ingest' Search { "ingest_type": "GMetaList", "ingest_data": { "gmeta": [ { "id": "filetype", "subject”: "https://search.api.globus.org/abc.txt", "visible_to": ["public"], "content": { "metadata-schema/file#type": "file” } }, ... ] }
- 29. Data ingest withGlobus Search 29 Search Index POST /index/{index_id}/ingest' Search { "ingest_type": "GMetaList", "ingest_data": { "gmeta": [ { "id": ”weight", "subject": "https://search.api.globus.org/abc.txt", "visible_to": ["urn:globus:auth:identity:46bd0f56- e24f-11e5-a510-131bef46955c"], "content": { "metadata-schema/file#size": ”37.6", "metadata-schema/file#size_human": ”<50lb” } }, ... ] } Visibility limited to Globus Auth identity - Single user - Globus Group - Registered client application
- 30. Data discovery withGlobus Search 30 { "@datatype": "GSearchResult", "@version": "2017-09-01", "count": 1, "gmeta": [ { "@datatype": "GMetaResult", "@version": "2019-08-27", "entries": [ { ... } ], "subject": "https://..." } ], "offset": 0, "total": 1 } GET /index/{index_id}/search?q=type%3Ahdf5 Search Index Simple query Search
- 31. Data discovery withGlobus Search 31 POST /index/{index_id}/search Search Index Complex query { "filters": [ { "type": "range", "field_name": ”pubdate", "values": [ { "from": "*", "to": "2020-12-31" } ] } ], "facets": [ { "name": "Publication Date", "field_name": "pubdate", ... } ] } Search
- 32. Working with Globus Search 32 jupyter.demo.globus.org Metadata,Search and Discovery
- 33.
- 34. Data (and compute)automation • 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
- 35. Automation with GlobusFlows • 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
- 36. Extending the ecosystem:Action providers 36 • 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
- 37. Working with Globus Flows 37 jupyter.demo.globus.org AutomationUsing Globus Flows
- 38. Coming soon: GlobusTrigger service • Trigger–Action platform • Predefined triggers and actions to create rules • Globus processes triggers and reliably executes actions
- 39.