35 lines
2.2 KiB
Markdown
35 lines
2.2 KiB
Markdown
# ThothII documentation
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ThothII is a human-reviewed datamart builder. It turns a question into validated SQL through an
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eight-phase workflow: the model proposes; a reviewer makes the decisions that are persisted.
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Start with the path that matches the work you need to do:
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| I need to… | Start here |
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| --- | --- |
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| Install or operate one instance | [Install and first start](install/first-start.md) |
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| Upgrade the server and integrate Omics Portal | [Codex server handoff](operations/server-codex-handoff.md) |
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| Choose full/embedded and configure the shell | [Shell and localization](operations/shell-and-localization.md) |
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| Reuse an authenticated server portal without a second login | [Upstream authentication](install/authentication-upstream.md) |
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| Understand how the two renderings share the same application | [Rendering architecture](architecture/application-shell.md) |
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| Validate login, logout and portal integration before release | [Acceptance matrix](testing/authentication-manual-acceptance.md) |
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| Add, update, or prepare a workspace | [Workspace operations](operations/workspaces.md) |
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| Ask a question and review the SQL workflow | [User guide](guida-utente.md) |
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| Configure and refresh an authoritative database catalog | [Database management](operations/database-management.md) |
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| Author and publish domain Evidence | [Evidence](evidence.md) |
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| Understand boundaries and persistence | [Architecture overview](architecture/overview.md) |
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## How the documentation is organised
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- **Install and operate** documents host-side setup, authentication, lifecycle, workspaces, and
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Pi administration.
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- **Use ThothII** documents the two application paths: reviewed NL→SQL sessions and administrative
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database management.
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- **Architecture and contracts** explain why the system behaves as it does and define the
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machine-facing boundaries. Consult them when integrating or changing an implementation; they
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are not a substitute for an operator runbook.
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The host-side `tht` command is the operator interface. The Python `tht` inside `harness/` is a
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different, internal workflow CLI invoked by the core. In examples, use an absolute installation
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descriptor path whenever discovery is not unambiguous.
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