mirror of
https://github.com/mims-harvard/ToolUniverse.git
synced 2026-09-19 07:31:47 +08:00
Shanghua Gao
08246bcd4d
* docs: expand redirect map with 15 additional legacy paths Adds redirects for paths uncovered in a second-pass audit against the live published site. Each destination verified to return HTTP 200 on https://zitniklab.hms.harvard.edu/ToolUniverse/. New /tutorials/ → /guide/, /tools/, /expand_tooluniverse/ redirects: - make_your_data_searchable, make_your_data_agent_searchable, build_search_and_share_datastores → guide/make_your_data_agent_searchable - skills → guide/skills_showcase - tool_finder → guide/finding_tools - overview → guide/index - remote_tools → tools/remote_tools - mcp_integration → expand_tooluniverse/remote_tools/mcp_integration Top-level legacy pages (404 at root, now redirected): - getting_started → guide/python_guide - deployment, contributing, changelog → about/<page> - faq → help/faq Local build confirms all 22 redirect stubs generate and that every destination file exists in the build output. * docs: fix broken sphinx-tabs, dead toctrees, orphan pages, missing image Build now produces 0 warnings/errors of these structural categories (down from ~280 such issues): - Re-enable sphinx_tabs.tabs extension (3.5.0 supports Sphinx 9.x); fixes 7 broken "Unknown directive type tabs" errors that made help/faq.html and help/troubleshooting.html render incomplete. - Drop 25+ dead toctree entries in api/modules.rst and api/tooluniverse.rst that referenced per-module pages never generated by sphinx-apidoc; modules.rst now points at the existing comprehensive tooluniverse autodoc page. - Wire 16 orphan pages into the master toctree so they're reachable from the navigation, including tooluniverse_case_study, visualization_tutorial, expert_feedback, literature_search_web_ui, euhealth, logging, openrouter, streaming, vllm, wechat_community, simbad_tools, the guide/index landing page, and the full expand_tooluniverse sub-tree. - Remove three stale ":doc:" links to old/{quickstart,installation, getting_started} from sitemap.rst (those directories are excluded from the build) and mark sitemap.rst as :orphan: since it's a parallel nav surface by design. - Mark MCP_TASKS_GUIDE.md as orphan and exclude the internal DOCUMENTATION_STRUCTURE.md meta-doc from the build. - Add the missing tools/remote/ui.jpg referenced by the remote expert_feedback page (previously: broken image). * docs: eliminate all 49 structural Sphinx ERRORs (broken tables, directives, headings) Round-3 build cleanup. Builds now finish with 0 structural ERRORs of any category (previous: 49 ERRORs spread across 20 files). Total warnings/errors dropped from 280 → 114; the remaining 114 are all in Python source-file docstrings (out of scope for a docs PR). Categories fixed: **Malformed tables** (8 files) Replace ASCII grid tables with mis-aligned pipes and inline-markdown pipe tables (which RST mis-parses as substitution references) with ``list-table`` directives that render correctly across all themes: - guide/literature_search_tools_tutorial.rst (two tables) - guide/cache_system.rst (env-var table whose first column overflowed) - guide/clinical_guidelines_tools.rst - guide/make_your_data_agent_searchable.rst - expand_tooluniverse/contributing/index.rst - expand_tooluniverse/contributing/remote_tools.rst - expand_tooluniverse/reference/index.rst **list-table indentation** (3 files) Option lines and list items were indented with 1 space (only valid for 3-space) so Sphinx silently dropped them and reported "exactly one bullet list expected": - guide/finding_tools.rst - guide/http_api.rst - guide/tools.rst **Code-block separators** (5 files, ~30 directives) Add the required blank line between an introductory paragraph and a following ``.. code-block::``. Without it, Sphinx treated the directive as a continuation of the paragraph and emitted "Unexpected indentation" for every line of the code: - guide/literature_search_tools_tutorial.rst - expand_tooluniverse/quick_start.rst - expand_tooluniverse/contributing/local_tools.rst - expand_tooluniverse/contributing/remote_tools.rst - guide/make_your_data_agent_searchable.rst **Heading-style + indentation** (3 files) - guide/building_ai_scientists/mcp_name_shortening.rst — strip stray leading spaces from two section titles + downgrade unknown ``.. critical::`` to ``.. important::`` - about/deployment.rst — remove rogue ``=========`` underline below numbered-list items that mis-led the parser into skipping heading levels - guide/make_your_data_agent_searchable.rst — extend four "title underline too short" underlines + convert four markdown ``` fences to RST literal blocks **Misc directive / target fixes** - guide/python_guide.rst — replace nonexistent ``.. success::`` with a tip-styled ``.. admonition::`` - guide/euhealth_tools_tutorial.rst — indent ``.. note::`` body so it is no longer an empty admonition - help/troubleshooting.rst — same fix + remove rogue ``=========`` line that was being read as a section overline - tools/cellosaurus_tools.rst — wrap ``CVCL_`` in literal backticks so the trailing underscore stops triggering missing-target lookups - expand_tooluniverse/index.rst — promote two leading-space bullet lists to standalone lists so the indentation is correct - expand_tooluniverse/reference/architecture.rst — switch ``.. graphviz::`` (extension not installed) to a plain ``.. code-block:: text``; the embedded content was Mermaid pseudo-code anyway - guide/tools.rst — strip leading space on a section title * docs: clear all remaining content warnings (lists, headings, refs, grids) Round-4 build cleanup. Builds now finish with 0 structural ERRORs and 0 content WARNINGs; the only remaining ~11 warnings are pre-existing autodoc infrastructure noise (duplicate object index entries from autosummary, and the ghost_tool / medrxiv_tool modules that genuinely fail to import) — none are in hand-written documentation. Fixes in this commit: **sphinx-design grids** (python_guide.rst) Re-indent two ``.. grid::`` blocks whose first card + options used 1-space indentation (Sphinx silently dropped them → "parent of grid-item should be grid-row"). Also fix a ``.. button-ref::`` whose content was indented 1 space, producing a broken ``:any:`` cross-reference, and point it at the absolute ``/api/modules``. **Numbered/bulleted sub-lists** (tool_composition, literature_search ×2, architecture, literature_search_web_ui, make_your_data, agentic_tools, finding_tools, euhealth) Insert the required blank line before nested lists and re-indent 1-space sub-bullets to align under their parent list marker. Clears ~80 "list ends without a blank line; unexpected unindent" warnings. **Title underlines** (logging, tool_caller, loading_tools, tool_composition, euhealth, make_your_data, contributing/local_tools, reference/index, remote_tools/tutorial, troubleshooting + bulk pass) Extend underlines shorter than their title text; strip stray leading spaces from section titles that Sphinx read as block quotes. **Stray markdown in RST** (make_your_data, local_tools) Convert leftover ``###`` headings and ``` ``` fences to proper RST directives; remove a rogue ``------`` separator that was being parsed as a section underline. **Duplicate autosectionlabel** (make_your_data) Rename the second "How it works" heading to "How sharing works". **uniprot_tools** (JSON + generated RST) Rephrase the ``min_length`` / ``max_length`` descriptions so the open-ended range syntax no longer contains a bare ``*`` that RST read as an unterminated emphasis marker. Fixed in the JSON source so it survives doc regeneration.
131 lines
3.9 KiB
ReStructuredText
131 lines
3.9 KiB
ReStructuredText
Cellosaurus Tools
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=================
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**Configuration File**: ``cellosaurus_tools.json``
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**Tool Type**: Local
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**Tools Count**: 3
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This page contains all tools defined in the ``cellosaurus_tools.json`` configuration file.
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Available Tools
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---------------
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**cellosaurus_get_cell_line_info** (Type: CellosaurusGetCellLineInfoTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Get detailed information about a specific cell line using its Cellosaurus accession number (``CVCL_``...).
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.. dropdown:: cellosaurus_get_cell_line_info tool specification
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**Tool Information:**
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* **Name**: ``cellosaurus_get_cell_line_info``
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* **Type**: ``CellosaurusGetCellLineInfoTool``
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* **Description**: Get detailed information about a specific cell line using its Cellosaurus accession number (``CVCL_`` format).
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**Parameters:**
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* ``accession`` (string) (required)
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Cellosaurus accession number (must start with ``CVCL_``)
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* ``format`` (string) (required)
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Response format
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* ``fields`` (array) (required)
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Specific fields to retrieve (e.g., ['id', 'ox', 'char']). If not specified, all fields are returned.
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "cellosaurus_get_cell_line_info",
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"arguments": {
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"accession": "example_value",
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"format": "example_value",
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"fields": ["item1", "item2"]
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}
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}
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result = tu.run(query)
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**cellosaurus_query_converter** (Type: CellosaurusQueryConverterTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Convert natural language queries to Solr syntax for Cellosaurus API searches. Uses semantic simil...
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.. dropdown:: cellosaurus_query_converter tool specification
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**Tool Information:**
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* **Name**: ``cellosaurus_query_converter``
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* **Type**: ``CellosaurusQueryConverterTool``
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* **Description**: Convert natural language queries to Solr syntax for Cellosaurus API searches. Uses semantic similarity to map terms to appropriate fields.
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**Parameters:**
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* ``query`` (string) (required)
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Natural language query to convert to Solr syntax (e.g., 'human cancer cells', 'HeLa cells from lung tissue')
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* ``include_explanation`` (boolean) (required)
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Whether to include detailed explanation of the conversion process
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "cellosaurus_query_converter",
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"arguments": {
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"query": "example_value",
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"include_explanation": true
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}
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}
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result = tu.run(query)
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**cellosaurus_search_cell_lines** (Type: CellosaurusSearchTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Search Cellosaurus cell lines using the /search/cell-line endpoint. Supports Solr query syntax fo...
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.. dropdown:: cellosaurus_search_cell_lines tool specification
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**Tool Information:**
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* **Name**: ``cellosaurus_search_cell_lines``
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* **Type**: ``CellosaurusSearchTool``
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* **Description**: Search Cellosaurus cell lines using the /search/cell-line endpoint. Supports Solr query syntax for precise field-based searches.
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**Parameters:**
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* ``q`` (string) (required)
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Search query. Supports Solr syntax for field-specific searches (e.g., 'id:HeLa', 'ox:9606', 'char:cancer'). See https://api.cellosaurus.org/api-fields for available fields.
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* ``offset`` (integer) (required)
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Number of results to skip (for pagination)
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* ``size`` (integer) (required)
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Maximum number of results to return
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "cellosaurus_search_cell_lines",
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"arguments": {
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"q": "example_value",
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"offset": 10,
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"size": 10
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}
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}
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result = tu.run(query)
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Navigation
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----------
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* :doc:`tools_config_index` - Back to Tools Overview
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* :doc:`../guide/loading_tools` - Loading Local Tools
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