PyFilesystem2 AnVIL plugin

A plugin for representing AnVIL resources in Python environments as a file system; particularly, in an AnVIL-launched Galaxy instances.

Galaxy installation requirements:

• file_sources_conf.yml in the Galaxy config directory with an AnVIL entry:

- doc: <whatever you would like to call it>
  id: <root folder name>
  namespace: <your google billing project == Terra namespace >
  type: anvil
  workspace: <name of the Terra workspace you wish to browse>
  api_url: <OPTIONAL - if not specified default production url will be used>
  on_anvil: <OPTIONAL - (true/false) must be true to manage AnVIL workload identity scopes>
  drs_url: <OPTIONAL - if not specified  default production url will be used>
  writable: <OPTIONAL - (true/false) if not specified plugin will be read-only>

NOTES:

• doc and id can be any string you choose but type MUST be anvil
• for off-AnVIL use, Galaxy and Data Fetch tools require the following environment variables:
  • GOOGLE_APPLICATION_CREDENTIALS="<path to credentials json>"
  • TERRA_NOTEBOOK_GOOGLE_ACCESS_TOKEN="$(gcloud auth print-access-token)"

Dependencies:

• FISS -- (Fi)reCloud (S)ervice (S)elector python library
• Google Cloud Python client library
• Google Cloud SDK
  • authenticated / configured with AnVIL project
• terra-notebook-utils
• gs-chunked-io
• getm