Forge Tools computational_review

computational_review read

scidex.forge.computational_review

Query a computational-review package (MyST-based review repository) and return a structured dry-run manifest of its contents: sections, bibliography entries, evidence packages, claims, conflicts, proposals, and figures. Does NOT write to the database — this is a read-only inspection verb. Source-backed per SPEC-191 P0 dry-run spec. Accepts a repository URL/commit or a local filesystem path.

HTTP: POST /api/scidex/forge/computational_review

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.computational_review``.",
  "properties": {
    "repository_url": {
      "anyOf": [
        {
          "maxLength": 512,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Public GitHub URL of the computational-review repository (e.g. ``https://github.com/AllenNeuralDynamics/ComputationalReviewRecurrence``). Used as bundle provenance when ``repo_path`` is not set.",
      "title": "Repository Url"
    },
    "commit_sha": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Exact Git commit SHA of the review package to query. If omitted and ``repo_path`` is set, uses the current HEAD of the local repo. If omitted and only ``repository_url`` is set, uses HEAD of the default branch.",
      "title": "Commit Sha"
    },
    "repo_path": {
      "anyOf": [
        {
          "maxLength": 1024,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Local filesystem path to a read-only computational-review repository. Mutually exclusive with ``repository_url``. Intended for dry-run testing with synthetic fixtures.",
      "title": "Repo Path"
    }
  },
  "title": "ComputationalReviewIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ClaimSummary": {
      "description": "An extracted claim from an evidence package.",
      "properties": {
        "claim_ref": {
          "description": "Proposed claim ref (e.g. ``claim:cl-abc123``).",
          "title": "Claim Ref",
          "type": "string"
        },
        "claim_text": {
          "default": "",
          "description": "Normalized claim text (≤600 chars).",
          "title": "Claim Text",
          "type": "string"
        },
        "source_path": {
          "default": "",
          "description": "Evidence JSON path.",
          "title": "Source Path",
          "type": "string"
        },
        "study_system": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Study system or domain.",
          "title": "Study System"
        },
        "replication_status": {
          "default": "unevaluated",
          "description": "Reported replication status: ``replicated``, ``unevaluated``, ``failed_replication``.",
          "title": "Replication Status",
          "type": "string"
        },
        "paper_refs": {
          "description": "Supporting paper refs.",
          "items": {
            "type": "string"
          },
          "title": "Paper Refs",
          "type": "array"
        }
      },
      "required": [
        "claim_ref"
      ],
      "title": "ClaimSummary",
      "type": "object"
    },
    "ConflictSummary": {
      "description": "An explicit evidence conflict turned into an open_question candidate.",
      "properties": {
        "open_question_ref": {
          "description": "Proposed open_question ref (e.g. ``open_question:oq-abc123``).",
          "title": "Open Question Ref",
          "type": "string"
        },
        "question_text": {
          "default": "",
          "description": "Conflict question text.",
          "title": "Question Text",
          "type": "string"
        },
        "source_path": {
          "default": "",
          "description": "Evidence JSON path.",
          "title": "Source Path",
          "type": "string"
        },
        "paper_refs": {
          "description": "Conflicting paper refs.",
          "items": {
            "type": "string"
          },
          "title": "Paper Refs",
          "type": "array"
        }
      },
      "required": [
        "open_question_ref"
      ],
      "title": "ConflictSummary",
      "type": "object"
    },
    "FigureSummary": {
      "description": "A visual artifact candidate from the figure registry.",
      "properties": {
        "visual_artifact_ref": {
          "description": "Proposed visual_artifact ref (e.g. ``visual_artifact:va-abc123``).",
          "title": "Visual Artifact Ref",
          "type": "string"
        },
        "figure_id": {
          "default": "",
          "description": "Figure identifier from registry.",
          "title": "Figure Id",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Figure title or caption.",
          "title": "Title",
          "type": "string"
        },
        "source_path": {
          "default": "",
          "description": "Figure file path in the repo.",
          "title": "Source Path",
          "type": "string"
        }
      },
      "required": [
        "visual_artifact_ref"
      ],
      "title": "FigureSummary",
      "type": "object"
    },
    "PaperRef": {
      "description": "Lightweight paper reference extracted from the review bibliography.",
      "properties": {
        "paper_ref": {
          "description": "SciDEX paper ref (e.g. ``paper:paper-abc123``).",
          "title": "Paper Ref",
          "type": "string"
        },
        "cite_key": {
          "default": "",
          "description": "BibTeX citation key.",
          "title": "Cite Key",
          "type": "string"
        },
        "doi": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "DOI if resolved.",
          "title": "Doi"
        },
        "pmid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PMID if resolved.",
          "title": "Pmid"
        },
        "title": {
          "default": "",
          "description": "Paper title.",
          "title": "Title",
          "type": "string"
        },
        "year": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Publication year.",
          "title": "Year"
        },
        "journal": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Journal or venue.",
          "title": "Journal"
        }
      },
      "required": [
        "paper_ref"
      ],
      "title": "PaperRef",
      "type": "object"
    },
    "ProposalSummary": {
      "description": "A gap-derived analysis or experiment proposal.",
      "properties": {
        "proposal_ref": {
          "description": "Proposed proposal ref (e.g. ``analysis_proposal:anprop-abc123``).",
          "title": "Proposal Ref",
          "type": "string"
        },
        "proposal_type": {
          "default": "analysis_proposal",
          "description": "``analysis_proposal`` or ``experiment_proposal``.",
          "title": "Proposal Type",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Proposal title.",
          "title": "Title",
          "type": "string"
        },
        "source_path": {
          "default": "",
          "description": "Evidence JSON path.",
          "title": "Source Path",
          "type": "string"
        },
        "source_question_ref": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Parent open_question ref.",
          "title": "Source Question Ref"
        }
      },
      "required": [
        "proposal_ref"
      ],
      "title": "ProposalSummary",
      "type": "object"
    },
    "SectionSummary": {
      "description": "A review section (wiki_page artifact candidate).",
      "properties": {
        "section_ref": {
          "description": "Proposed wiki_page ref (e.g. ``wiki_page:review-synthetic-review-01_intro``).",
          "title": "Section Ref",
          "type": "string"
        },
        "title": {
          "default": "",
          "description": "Section heading title.",
          "title": "Title",
          "type": "string"
        },
        "source_path": {
          "default": "",
          "description": "Relative path in the review repo.",
          "title": "Source Path",
          "type": "string"
        },
        "source_url": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "GitHub URL to the source file at the given commit.",
          "title": "Source Url"
        },
        "citation_anchor_count": {
          "default": 0,
          "description": "Number of citation anchors found in this section.",
          "title": "Citation Anchor Count",
          "type": "integer"
        },
        "word_count": {
          "default": 0,
          "description": "Approximate word count of the section.",
          "title": "Word Count",
          "type": "integer"
        }
      },
      "required": [
        "section_ref"
      ],
      "title": "SectionSummary",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.computational_review``.",
  "properties": {
    "bundle_ref": {
      "default": "",
      "description": "Proposed analysis_bundle ref (e.g. ``analysis_bundle:ab-abc123``).",
      "title": "Bundle Ref",
      "type": "string"
    },
    "title": {
      "default": "",
      "description": "Review package title.",
      "title": "Title",
      "type": "string"
    },
    "repository_url": {
      "default": "",
      "description": "Source repository URL.",
      "title": "Repository Url",
      "type": "string"
    },
    "commit_sha": {
      "default": "",
      "description": "Git commit SHA used.",
      "title": "Commit Sha",
      "type": "string"
    },
    "source_policy_mode": {
      "default": "",
      "description": "Source policy applied (e.g. ``public_source_pointer_with_short_context``).",
      "title": "Source Policy Mode",
      "type": "string"
    },
    "counts": {
      "additionalProperties": {
        "type": "integer"
      },
      "description": "Counts of parsed artifacts: papers, wiki_pages, claims, open_questions, analysis_proposals, experiment_proposals, visual_artifacts, evidence_links, artifact_links.",
      "title": "Counts",
      "type": "object"
    },
    "papers": {
      "description": "Bibliography entries resolved from BibTeX.",
      "items": {
        "$ref": "#/$defs/PaperRef"
      },
      "title": "Papers",
      "type": "array"
    },
    "sections": {
      "description": "Review section summaries (wiki_page candidates).",
      "items": {
        "$ref": "#/$defs/SectionSummary"
      },
      "title": "Sections",
      "type": "array"
    },
    "claims": {
      "description": "Extracted claim summaries.",
      "items": {
        "$ref": "#/$defs/ClaimSummary"
      },
      "title": "Claims",
      "type": "array"
    },
    "conflicts": {
      "description": "Conflict-derived open question summaries.",
      "items": {
        "$ref": "#/$defs/ConflictSummary"
      },
      "title": "Conflicts",
      "type": "array"
    },
    "proposals": {
      "description": "Gap-derived proposal summaries.",
      "items": {
        "$ref": "#/$defs/ProposalSummary"
      },
      "title": "Proposals",
      "type": "array"
    },
    "figures": {
      "description": "Figure registry summaries (visual_artifact candidates).",
      "items": {
        "$ref": "#/$defs/FigureSummary"
      },
      "title": "Figures",
      "type": "array"
    },
    "error": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Error message if the package could not be parsed. Null on success.",
      "title": "Error"
    },
    "took_ms": {
      "description": "Wall-clock time for the parsing operation.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ComputationalReviewOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/computational_review' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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