Ready Tools On Sciminer

Ready Tools on SciMiner

This skill handles arbitrary SciMiner tools whose API descriptions are published under https://sciminer.tech/tool_api_files/. When a user asks to use a specific SciMiner tool, this skill retrieves the tool-doc index, resolves the matching Markdown file, reads the document, and writes or runs invocation code from the selected document's exact fields.

SciMiner calls must read the API key from ~/.config/sciminer/credentials.json and send it as the X-Auth-Token, and user-facing summaries must include the returned share_url for each successful task.

When to use this skill

• The user names a SciMiner tool and wants it invoked.
• The user asks how to call a specific SciMiner tool from code.
• The user wants the exact parameters, enums, file-upload behavior, or payload shape for a SciMiner tool.
• The user wants a shareable SciMiner result link after submission.

Tool discovery rule

• Start from https://sciminer.tech/tool_api_files/.
• Treat the index page as the source of available SciMiner tool docs.
• Prefer exact, case-insensitive matching between the requested tool name and the linked file stem before _api_doc.md.
• Use the actual link returned by the index instead of constructing a guessed URL.
• If multiple tools plausibly match, ask the user to choose.
• If no match is found, report that the tool is not present in the current SciMiner tool-doc index.

Examples:

• ADMET Predictor -> ADMET Predictor_api_doc.md
• AutoDock Vina -> AutoDock Vina_api_doc.md
• Graph-pKa -> Graph-pKa_api_doc.md

Authoritative payload source

The selected Markdown file under https://sciminer.tech/tool_api_files/ is the single source of truth for the chosen tool. The agent MUST:

1. Read the selected tool doc before every invocation.
2. Never invent provider_name, tool_name, parameter names, enum values, content type, submission flow, or upload-field names from memory.
3. Extract and follow the document's exact:
   • Base URL
   • API endpoint
   • Content-Type
   • Authentication header
   • Tool Name

• Section-level tool method
• Parameter table, including required fields and enum values
• File-upload instructions and example submission payload structure

1. Select the correct variant if the doc contains multiple tool sections (for example, single-item vs batch, SMILES vs file input).
2. Reject or drop user-provided parameters that are absent from the selected doc section, with a brief explanation.

Prerequisites

1. Obtain a free SciMiner API key from https://sciminer.tech/utility.
2. Store it outside this repository at ~/.config/sciminer/credentials.json with JSON shaped as {"api_key":"your_api_key_here"}.
3. For SciMiner calls, read the API key from ~/.config/sciminer/credentials.json and send it as the X-Auth-Token header.
4. Never print, persist, or store the API key in prompts, logs, or repository files. Agents should remember only the credential file path.

If ~/.config/sciminer/credentials.json is not available or does not contain an api_key field, stop and tell the user to obtain a free SciMiner API key from https://sciminer.tech/utility and store it in that file. Do not try to complete the task by switching to other tools or services.

Required workflow

1. Read the index at https://sciminer.tech/tool_api_files/.
2. Resolve the Markdown description file for the requested tool from the links actually present in the index.
3. Read the full Markdown document for the resolved tool.
4. Choose the tool section that matches the user's request shape.
5. Collect any missing required parameters from the user.
6. Upload any required file inputs and replace local paths with returned file_id values.
7. Submit the job using the exact provider_name, tool_name, endpoint, content type, and parameter names from the selected doc, following the document's example submission flow.
8. Poll for the task result.
9. Return the share_url in the final user-facing summary.

Write the invocation code directly from the selected Markdown document's base information block, parameter table, file-upload instructions, and example code. Do not apply a shared invocation template in this skill.

File-upload rules

• Upload every required file parameter described by the selected Markdown doc before invocation.
• Replace local file paths in parameters with the returned file_id strings.
• Use the upload form field described by the selected doc. If the doc shows only the generic SciMiner upload example and does not override the form field, use file.
• Skip optional file parameters that the user did not provide.

Expected result format

{
  "status": "SUCCESS",
  "result": {"...": "..."},
  "task_id": "xxx",
  "share_url": "https://sciminer.tech/share?id=xxx&type=API_TOOL"
}

Reporting rules

• Cite the selected Markdown doc under https://sciminer.tech/tool_api_files/ as the payload source in your summary.
• Attach the share_url of every successful task at the end of the response so the user can view the online result.
• If polling reaches 600 seconds and the task is still running, stop polling and return the current task_id and share_url so the user can check later.
• Do not return raw file-download links when a share_url is available.
• Do not expose the API key in code snippets, logs, or summaries.

Notes

• This skill is intentionally generic. It should not hard-code tool-specific payload schemas beyond what the selected SciMiner Markdown doc states.
• The tool-doc index currently exposes Markdown files named _api_doc.md; rely on the live index rather than assuming the file exists.
• When the user asks to "use tool X", the first action is to resolve and read tool X's Markdown doc, not to infer parameters from memory.
• This skill defines its own credential and share_url handling rules and does not rely on another skill document.