inno-prepare-resources

name	inno-prepare-resources
description	Loads the evaluation instance, searches GitHub for related repositories, builds a dataset description, queries the Prepare Agent for reference codebases, and downloads arXiv paper sources. Covers both Idea mode and Plan mode (the only difference is whether innovative ideas are included in the Prepare Agent query).

Inno Prepare Resources

Inputs

Read from instance.json. Path values are absolute when the project is created by Dr. Claw; use as-is. If relative (e.g. hand-edited), resolve with path.join(project_path, value).

Parameter	Required	Description
instance	Yes	Path to the instance JSON file (absolute in Dr. Claw). Use as-is to read the file. File contains source_papers, task1/task2, etc.
task_level	Yes	Which task field to read from the instance — "task1" (Plan) or "task2" (Idea)
Ideation.references	Yes	Path to Ideation references dir (absolute in Dr. Claw) — for downloaded papers and prepare logs
Experiment.code_references	Yes	Path (absolute in Dr. Claw) — for cloned repos
Experiment.datasets	Yes	Path (absolute in Dr. Claw) — for dataset files
category	Yes	Research category tag (e.g. nlp_qa, gnn, recommendation). Used to locate the built-in dataset metaprompt
references	Yes	A pre-formatted string listing all source papers from the instance
context_variables	Yes	Shared context dictionary; this step will write date_limit into it
ideas	No	Full innovative-idea / plan text. Provide only in Plan mode — when present the Prepare Agent query includes the ideas for more targeted repo selection
dataset_description	No	Pre-built dataset description from the orchestrator (for custom / user-provided datasets). When provided, skip the metaprompt import in Step 3

Outputs

Output	Description
prepare_res	Full text response from the Prepare Agent (contains selected reference repositories and reasoning)
download_res	Result log from downloading arXiv paper sources to local disk
dataset_description	Composed prompt string describing the datasets, baselines, comparisons, and evaluation metrics
data_module	The imported metaprompt module object (Idea mode). In Plan mode this is not returned
context_variables	Updated with date_limit (str, YYYY-MM-DD)

Cache file outputs

Every intermediate result must be persisted as a JSON file under Ideation/references/logs/. The directory layout follows:

Ideation/references/logs/
├── load_instance.json                  ← written by orchestrator
├── github_search.json
├── download_arxiv_source_by_title.json
└── prepare_agent.json

Ideation/references/logs/load_instance.json is written by the orchestrator before this skill runs — do not overwrite it.

Tool cache format (tools/*.json)

Each tool output file records the function call arguments and result:

{
  "name": "<tool_name>",
  "args": { ... },
  "result": <result_value>
}

github_search.json — written after Step 2:

{
  "name": "github_search",
  "args": {
    "metadata": {
      "source_papers": [ ... ],
      "task_instructions": "...",
      "date_limit": "YYYY-MM-DD"
    }
  },
  "result": "<concatenated github_result string>"
}

download_arxiv_source_by_title.json — written after Step 6:

{
  "name": "download_arxiv_source_by_title",
  "args": {
    "paper_list": ["paper title 1", "paper title 2"],
    "references_path": "<instance.Ideation.references if absolute, else path.join(project_path, instance.Ideation.references)>"
  },
  "result": "<download result log string>"
}

Agent cache format (agents/*.json)

Each agent output file records the final context variables (no conversation messages):

{
  "context_variables": {
    "references_path": "<use instance.Ideation.references as-is if absolute, else path.join(project_path, ...)>",
    "code_references_path": "<use instance.Experiment.code_references as-is if absolute, else path.join(project_path, ...)>",
    "datasets_path": "<use instance.Experiment.datasets as-is if absolute, else path.join(project_path, ...)>",
    "date_limit": "YYYY-MM-DD",
    "prepare_result": {
      "reference_codebases": ["repo1", "repo2"],
      "reference_paths": ["Experiment/code_references/repo1", "Experiment/code_references/repo2"],
      "reference_papers": ["paper title 1", "paper title 2"]
    }
  }
}

prepare_agent.json — written after Step 4–5. Contains the final context_variables with prepare_result holding reference_codebases, reference_paths, and reference_papers.

Step-by-step Instructions

Step 1 — Load the evaluation instance

Call load_instance(instance.instance, task_level) — when created by Dr. Claw, instance.instance is already absolute; otherwise resolve with path.join(project_path, instance.instance).

This reads the instance JSON and returns an EvalMetadata object containing:

• source_papers — list of dicts, each with reference, rank, type, justification, usage
• task_instructions — the task description text (from the field named by task_level)
• date_limit — the publication date of the target paper (fetched from arXiv via the instance url); defaults to "2024-01-01" if metadata cannot be retrieved

Write date_limit into context_variables["date_limit"].

Note: Ideation/references/logs/load_instance.json should already exist — it was written by the orchestrator. If not, write it now following the tool cache format.

Graceful handling: If the instance JSON was constructed by the orchestrator and has no url or an empty source_papers list, use a sensible default date_limit and continue — do not raise an error.

Step 2 — Search GitHub for related repositories

Call github_search(metadata).

Iterate over every entry in metadata["source_papers"]. For each paper, use its reference (title) as the search query and call the GitHub Search Repositories API:

GET https://api.github.com/search/repositories?q=<paper_title>&per_page=10&page=1

From each result item, extract:

• name: {owner}/{repo}
• description: repository description
• link: html_url

Format each paper's results as a human-readable block:

Here are some of the repositories I found on GitHub:
    Name: owner/repo
    Description: ...
    Link: https://github.com/owner/repo

Concatenate all papers' results into a single github_result string, using a ****************************** separator between papers.

Rate-limit handling: wait ~2 seconds between consecutive GitHub API calls to avoid HTTP 403 throttling. The last paper does not need a delay.

Fallback when source_papers is empty: use keywords extracted from task_instructions as the search query instead, and perform a single GitHub search call to find relevant repositories.

Save → Ideation/references/logs/github_search.json

Step 3 — Build the dataset description

Choose one of the following strategies (in priority order):

1. Orchestrator override — if dataset_description was passed as input, use it directly.

2. Built-in metaprompt — if category maps to an existing metaprompt module, import it and compose the description from its five fields:

   • TASK — what the task is about
   • DATASET — dataset files, structure, and loading instructions
   • BASELINE — representative baseline methods
   • COMPARISON — performance comparison table
   • EVALUATION — evaluation metrics and scoring functions
   • REF — additional references and notes

   The composed description follows this template:

   You should select SEVERAL datasets as experimental datasets from the following description:
   {DATASET}
   
   We have already selected the following baselines for these datasets:
   {BASELINE}
   
   The performance comparison of these datasets:
   {COMPARISON}
   
   And the evaluation metrics are:
   {EVALUATION}
   
   {REF}
   

3. Manual / minimal — if neither of the above is available, construct a minimal description from what is known about the task (e.g. from task_instructions), or ask the user for additional information.

Also retain the data_module object (the imported metaprompt module) for later use in Idea mode.

Step 4 — Query the Prepare Agent

Build the query depending on mode:

• Idea mode (no ideas provided):

  You are given a list of papers, searching results of the papers on GitHub.
  List of papers:
  {references}
  
  Searching results of the papers on GitHub:
  {github_result}
  
  Your task is to choose at least 5 repositories as the reference codebases.
  Note that this time there is no innovative ideas, you should choose the
  most valuable repositories as the reference codebases.
  

• Plan mode (ideas provided):

  You are given a list of papers, searching results of the papers on GitHub,
  and innovative ideas according to the papers.
  List of papers:
  {references}
  
  Searching results of the papers on GitHub:
  {github_result}
  
  innovative ideas:
  {ideas}
  
  Your task is to choose at least 5 repositories as the reference codebases.
  

Send the query to the Prepare Agent and record the full response as prepare_res.

Save → Ideation/references/logs/prepare_agent.json (final context_variables only, no messages)

Step 5 — Extract reference paper list

Parse prepare_res to extract a JSON object containing "reference_papers" (a list of paper title strings the agent selected).

Use bracket-matching JSON extraction — find the first complete {…} in the text, parse it, and read reference_papers.

Fallback: if reference_papers is empty (e.g. the agent found no GitHub repos and returned nothing), fall back to the original source_papers titles from the instance metadata so that paper download can still proceed.

Step 6 — Download arXiv paper sources

Call download_arxiv_source_by_title(paper_list, references_path) where references_path is instance.Ideation.references (absolute in Dr. Claw) or path.join(project_path, instance.Ideation.references) if relative.

This searches arXiv for each paper title, downloads the LaTeX / source archive, and extracts it into Ideation/references/papers/. Record the result log as download_res.

Save → Ideation/references/logs/download_arxiv_source_by_title.json

Checklist

• load_instance called; date_limit written to context_variables (default used if unavailable)
• github_search completed; result saved → Ideation/references/logs/github_search.json
• dataset_description built (from orchestrator override, built-in metaprompt, or manual construction)
• Prepare Agent queried; conversation saved → Ideation/references/logs/prepare_agent.json
• reference_papers extracted from Prepare Agent output; fallback to source papers if empty
• arXiv paper sources downloaded to Ideation/references/papers/; result saved → Ideation/references/logs/download_arxiv_source_by_title.json
• All cache files written under Ideation/references/logs/