Overture docs update - #1089
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Arranger's docs covered SQON, introspection, concepts, and the query flow, but had no reference for the GraphQL query API itself (the endpoint, an example query + response, the hits/aggregations shape). Add usage/graphql-api.md documenting POST /graphql, the per-catalogue document-type root with hits and aggregations, the Sort input, the dot->__ field-name convention, and schema discovery via the Introspection API. Cross-link it from Query Processing. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Keeps the docs PR limited to documentation; .dev working notes will land separately.
The site renamed /docs/core-software/* to /build/* to /develop/*, moved /docs/contribution to /develop/contributing, /guides/getting-started to /deploy, and /guides/administration-guides to /use. Each old path only resolved through a redirect hop. Verified every new target against a local site build.
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| The current scaffold implements the Streamable HTTP MCP transport using **v1.x** of the official [MCP TypeScript SDK](https://github.com/modelcontextprotocol/typescript-sdk/tree/v1.x). | ||
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| ## Tools |
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these tool names are stale: the MCP server registers them as snake_case, not kebab-case.
- list-catalogues should be list_catalogues
- get-sqon-schema should be get_sqon_schema
- get-catalogue-fields should be get_catalogue_fields
- execute-query should be execute_query
these were renamed to snake_case in #1088. The PR description says this branch already rebased past that change, so it looks like this new table just didn't pick up the rename when it was written
| - **[Arranger Overview](https://docs.overture.bio/docs/core-software/Arranger/overview)** | ||
| - [**Setting up the Development Enviornment**](https://docs.overture.bio/docs/core-software/Arranger/setup) | ||
| - [**Common Usage Docs**](https://docs.overture.bio/docs/core-software/Arranger/setup) | ||
| - **[Arranger Overview](https://docs.overture.bio/develop/Arranger/overview)** | ||
| - [**Setting up the Development Environment**](https://docs.overture.bio/develop/Arranger/setup) | ||
| - [**Reference Docs**](https://docs.overture.bio/develop/Arranger/reference) |
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since this content already lives in the same repo, three of these links could point at it directly instead of the docs site:
- Arranger Overview (line 15) to ./docs/overview.md
- Setting up the Development Environment (line 16) to ./docs/setup.md
- Reference Docs (line 17) to ./docs/reference/reference.mdx.
one tradeoff worth knowing: docs/reference/reference.mdx and the pages it links to use Docusaurus-specific syntax (the DocCardList component, ::: admonition blocks), which renders as plain text on GitHub rather than the docs site's styled callouts, still fully readable, just less polished
... your call on these.
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updated, went with all three in-repo
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| - For support, feature requests, and bug reports, please see our [Support Guide](https://docs.overture.bio/community/support). | ||
| - For detailed information on how to contribute to this project, please see our [Contributing Guide](https://docs.overture.bio/docs/contribution). | ||
| - For detailed information on how to contribute to this project, please see our [Contributing Guide](https://docs.overture.bio/develop/contributing). |
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on the other hand, this Contributing Guide link (line 30) could similarly point at ./CONTRIBUTING.md, which already exists at the repo root with matching content, and would be directly relevant to Arranger's own specific contributions rather than a generic Overture.
I dare say that should be the priority for this specific link, across all repos, because each repo has nuances that are not "generic" as non-devs may imagine can be.
...but importantly: GitHub also gives root-level CONTRIBUTING.md special treatment (it's auto-surfaced on new issues and PRs), so linking to it directly is arguably more useful than the external link, not just an equivalent swap at all.
for contrast, the Support Guide and quickstart guides links are fine left as-is, since that content is org-wide or platform-wide and doesn't live in this repo
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Keeping it to Arranger in this PR but will update across the board
Documentation for the Overture docs site, plus factual corrections to two in-repo READMEs. No source code changes.
Three new pages, a restructure of
docs/usage/intodocs/reference/, and three corrections to thegraphql-routerREADME's network-search section.New pages
docs/reference/graphql-api.mdsidebar_position: 2.5)POST /graphqlendpoint, SQON and field selection, pagination, sorting, and a pointer to the Introspection API for runtime field discoverydocs/charts.mdsidebar_position: 4)modules/charts/README.md, coveringChartsProviderbatching every registered chart into one GraphQL query, plus three screenshotsdocs/federated-search.mdsidebar_position: 6)modules/graphql-router/src/network/, not from the READMEThe federated search page is new coverage, not a port. A sweep of all 74 remote branches found no dedicated page anywhere, only scattered mentions plus an unmerged 2024 design doc on
origin/search-docswhose design has since diverged from what shipped. The page states up front that federation returns aggregate counts, not documents (there is no federatedhitslist), and records that the feature appears under three names: federated search, network search, and network aggregation, withnetworkbeing what configuration and GraphQL field names use.Restructure
docs/usage/*becomesdocs/reference/*, andusage.mdxbecomesreference.mdx.docs/usage/06-ai-and-automation.mdbecomesdocs/mcp-server.md, promoted out of the reference section to a top-level "Arranger MCP server" page.docs/migration/v3.1.mdbecomesdocs/reference/08-Migration/v3.1.md.07-defaults-and-limitsto06,08-feature-flagsto07.overview.md,setup.md,reference.mdx,02-query-processing.md,06-defaults-and-limits.mdandgraphql-api.md.docs/overview.mdalso gains a Key Features bullet and a federation pathway;01-arranger-configs.mdnotes the optional fifth config file (network.json);05-introspection.md,07-feature-flags.mdandcharts.mdgain federation cross-links.Corrections to
modules/graphql-router/README.md, Network searchThree statements were wrong against the code in
src/network/:___aggregation_not_available___sentinel bucket rather than dropping the field.remoteRequests.headersandremoteNodes[].requests.headerswere presented asarrangerRouteroptions. They aresearch-serverconfig-file properties, normalized into acustomizeRemoteRequestfunction, so passing them to the library directly is a silent no-op. Per-node headers also replace the global list rather than merging with it.documentType: 'FileAggs', which resolves toFileAggsAggregationsand fails discovery.apps/mcp-server/README.mdis updated for the docs-site URL change.Rebased onto
mainCurrent with
main, no conflicts. 11 commits absorbed, four resolved:snake_caseInstead ofkebab-case#1088 renamed them to snake_case onmainwhile this branch still had kebab-case, somainwins on both the tool list and the fullerexecute_querysignature, verified againstapps/mcp-server/src.docs/mcp-server.mdwas combined, keepingmain's newquery_arrangerPrompts block from ✨ Addquery-arrangerSystem Prompt and MCP Serverinstructions(overture-stack/admin#184) #1087 alongside this branch's heading promotion out ofreference/..dev/files follow this branch's ownchore: drop .dev changescommit, so.dev/matchesmainexactly. The exception istech-debt.md, where both entries are kept because they are additive: this branch's OpenSearch entry records why its Makefile change removes thestart-ostarget.mainalso landed eightgraphql-routerchanges around catalogue availability.docs/reference/05-introspection.mdalready documents the resultinghealthy/degraded/unhealthyandavailable/failedvalues and all six error codes, each confirmed present in the code, so that page needed no update.Before merging