Storing and Organizing Data¶

Rough demo outline

1. Automatic ingest from a POSIX directory to Keep
   • Ingestor's access to staging area (could be remote NFS or sshfs mount) is arranged ahead of time
   • 3rd-party's access to staging area is arranged ahead of time
   • Ingestor runs in a screen session. Command line parameters provide project (group/folder) ID and a tag that indicates "this is for me to ingest".
   • Someone ("3rd-party") uploads some files to the staging area via SFTP or whatever
   • 3rd-party does an API call to "ingest-notify app". This might be a short bash script culminating in a curl command. In the API call, the 3rd-party provides a label (e.g., a sample ID) and a list of files, checksums, and an arbitrary "properties" hash containing whatever the 3rd-party wants.
   • Ingest-notify app generates a "data in staging area is ready to ingest" event via API server.
   • Ingestor waits of a "data in staging area is ready to ingest" notification via API server.
   • Ingestor reads the data from the staging area and writes it into Keep (creates one collection per API call made by 3rd-party).
   • Ingestor (or arv-put on behalf of ingestor?) makes API calls while working, to indicate progress (bytes done/todo). arvados.v1.logs.create(object_uuid=uuid_of_upload_object)
   • In Workbench the imported Datasets appear as Collections in the designated project
   • After data has been copied into Keep, ingestor deletes the files from the staging area (if --delete-after flag given).
     ...
2. My data gets into the right project as specified by the uploader (API call)
   • How is the staging-area ↔ project mapping specified, and how/where is it encoded/stored?
     ...
3. Subscribe to notifications (by email and/or Workbench dashboard): when files start/finish uploading; when files are shared with customer; when files are downloaded by third party
   • For now, use existing Logs table + automatic logging of create/update/delete operations + "progress" event from arv-put (see above)
   • "Show project" page shows recent activity: one progress bar for each unfinished upload, one entry for each start/finish event.
   • Dashboard page shows recent activity from all of my projects.
     ...
4. Move/copy collections between projects (Project RX1234, or Customer X’s files), tag them in destination project with the appropriate string (e.g., sample ID) -- defaulting to existing tag used in source project (e.g., provided at time of upload).
   • UI for presenting Groups as Projects/Folders: create, view, rename, share, delete
   • UI for copying/moving objects between folders
   • How to avoid confusion about "is this one object in two places, or are there two objects?" Note GDocs has a bit of both, "My Drive" / "Shared with me" vs. regular folders
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5. Share project with other users/groups
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6. “Anyone with this secret link can view/download” mode. Enable, disable, change magic link. Use cases: browser + “wget -r”.
   • Perhaps the secret in the secret link is an ApiClientAuthorization token, belonging to the person creating the link, scoped to a single project/collection
   • How do we implement "Anonymous user, not logged in"?
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7. See log/overview of who has accessed your shared data (incl. “anonymous user” if using secret-link-to-share); when shared/unshared; when each upload started/finished -- for a single project, and across all projects
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8. Pilot alternate Workbench group/dashboard view
   ...

Retrospective notes¶

• Went well - still some merge-race at the end
• Lots of branches going in
• Not a lot of merge conflicts
• Big spec change (rejecting "ingestor" story in favor of future "remote arv-put")
• Some in-sprint deployment dependency stuff (crunch+docker, websockets)
• Please tag commits with story numbers. Use "refs #1234" for merges. (Use "refs #1234" for individual commits too?)
• Consider extracting a task into a story if it grows into its own thing (e.g., token handling as part of collection sharing)
• In sprint review, include 2 more agenda items: summary of things not done + high-level overview of next sprint
• How to improve support/feedback loop for beta users?