Import a genome in IntelliNix

Status

• Needs an IntelliNix workspace with the genome flags on Import in Settings, Workspace policy, Transfer. Preview, consent and undo. The Transfer section appears only when the agent_genome and genome_format flags are on for the workspace, and only an administrator can import.

Prerequisites

• An IntelliNix workspace where the agent_genome and genome_format flags are on. Both are feature flags, and the Transfer screen is built but off by default. Ask whoever manages your workspace.
• An account that can change workspace settings (an administrator).
• A genome file of at most 256 KB and 200 genes. Verify it first (install page).
• For genes in other layers: genome_hierarchy for the workspace and personal layers, genome_teams as well for team genes, genome_shared for the shared layer. Genes for a layer that is off are skipped, and the preview says so.

The steps

The words in quotes are labels on the screen.

1. Sign in to IntelliNix as a workspace administrator, then open Settings, then "Workspace policy". Have my-genome.agf.json ready.
2. Find the "Transfer" section and its "Import" part. If the section is not there, the genome flags are off for your workspace (see the prerequisites).
3. Under "Import into", choose "This workspace’s rules only" or one of your agents.
4. Under "File to import", choose the file. The limit is 256 KB and 200 entries. A bigger or invalid file is rejected and nothing is imported.
5. Read the preview table. Each entry says where it goes and what happens: "Will be added", "Needs review" (a learned gene becomes a proposal) or "Ignored" with a reason. Nothing has been applied yet, and the preview expires in 7 days.
6. Tick the consent box, then use the import button ("Import to this workspace"). If the preview holds personal-layer entries, only the administrator who made it can apply it.
7. To take it back, use "Undo this import" and then "Undo import". If lists changed after the import, the screen warns you first.

What you should see

• After you choose the file: a table with one row per gene. Its columns are Entry, Where it goes and What happens.
• A line such as “N will be added, N need review, N ignored.” and the note “Built-in rules and identity are never imported.”
• After you import: “Entries added: N. Needing review: N.”
• After you undo: “The entries this import added were removed.”

Reasons you may see in the “What happens” column for a gene that is left out:

• needs_agent: Customer and learned genes need an agent to import into. A workspace import has none.
• layer_flag_off: The layer these genes belong to is not turned on in your workspace.
• team_not_chosen: The file has team genes and no team was chosen.
• layer_unavailable: The personal layer is not available to you.
• id_conflict: A different gene with the same id is already there. Nothing is overwritten.

Before the import: check the file

# Linux
echo '[PUBLISHED-SHA256]  my-genome.agf.json' | sha256sum --check -
# macOS
echo '[PUBLISHED-SHA256]  my-genome.agf.json' | shasum -a 256 --check -

The same thing by script

The screen calls the same routes you can call yourself. See the REST guide. A short form:

# 1. Preview. This writes only a transfer record. Nothing is applied.
#    Into the workspace layers only:
curl -sS -X POST '[YOUR-INTELLINIX-API]/genome/workspace/import/preview' \
  -H 'X-API-Key: [YOUR-API-KEY]' \
  -H 'Content-Type: application/json' \
  --data-binary '@my-genome.agf.json'

#    Or into one agent and the workspace layers:
curl -sS -X POST '[YOUR-INTELLINIX-API]/genome/agents/[AGENT-ID]/import/preview' \
  -H 'X-API-Key: [YOUR-API-KEY]' \
  -H 'Content-Type: application/json' \
  --data-binary '@my-genome.agf.json'

# 2. Read the answer. Copy its "id" into [TRANSFER-ID] below, then read "genes", "skipped" and "rejected".
#    Apply only if you agree with every line.
curl -sS -X POST '[YOUR-INTELLINIX-API]/genome/transfers/[TRANSFER-ID]/consent' \
  -H 'X-API-Key: [YOUR-API-KEY]'

# 3. To undo the import in one step:
curl -sS -X POST '[YOUR-INTELLINIX-API]/genome/transfers/[TRANSFER-ID]/undo' \
  -H 'X-API-Key: [YOUR-API-KEY]' \
  -H 'Content-Type: application/json' \
  -d '{"confirm_later_changes":false}'

Troubleshooting

If the Transfer section is missing, the flags are off for your workspace. The page then shows that workspace policy is not turned on, or shows no Transfer section.

These screen words were read from the IntelliNix source. The screens were not tried in a running workspace, so a label may differ slightly in your version.