literature-review-paper-screener

Literature Review Paper Screener V1.4.6. The local agent (internet-enabled, free) searches for literature, collects evidence, builds per-paper Evidence Records with Evidence Availability Levels A-D, submits ONE paper per workbook row to the private LoomLoom Cloud template (rows run as independent parallel tasks, so screening never exceeds the platform per-activity timeout), then audits and merges the returned screening results and renders Excel Paper Sheet + Reading List. Cloud has no internet access; you gather the evidence and it evaluates it. Use it for Literature Review tasks in the Medical Science focus only; do not use it as a general citation manager, for other task types, or for disciplines it is not configured for. The bundled files are local helpers only — a pre-flight checker, a result validator, and an Excel renderer. All searching, downloading, and cloud submission is performed by the agent through the loomloom CLI, which this skill requires.

Literature Review Paper Screener — Local Agent Skill (V1.4.6)

The Local Agent is the internet research layer of the Literature Review Paper Screener. You have internet access and do all research and evidence gathering. The Cloud (a private LoomLoom template) has no internet access; it screens and organizes only the evidence you send it.

Core principle: Local Agent gathers the evidence. Cloud evaluates and organizes the evidence. (Full product rules live in the project documentation set; this Skill is the executable guide.)

What one task means and how it executes (V1.1)

One task = one full literature review for one student topic, delivered as:

• Paper Sheet — the complete screened pool, one row per retained paper (evidence level, screening verdicts, priority, reading role, evidence-bound notes/summary)
• Reading List — the same pool organized by Priority and Primary Reading Role

Execution model (per-paper rows): the Cloud template's screening step has a platform-fixed per-activity timeout. Screening all N papers inside one activity times out for larger sets (observed: 20 papers → StartToClose timeout failure, twice). V1.1 therefore submits one paper per workbook row: N papers = N rows = N independent parallel cloud tasks, each screening a single paper in seconds. The results are merged locally back into one Paper Sheet + Reading List.

• Never put more than one paper's evidence into a single workbook row.
• Total cloud tasks = total papers = total per-task fee units (Market: USD 0.10/task).
• Merging is local-only: no cloud aggregation step, no re-derivation.

Prerequisites

• Python 3.9+ (validator/render scripts)
• loomloom Skill + CLI installed and loomloom doctor reports healthy=true
• A CogFoundry (or configured) LoomLoom account with balance for cloud runs

Bundled files and what each one does

This package ships documentation and three local helper scripts. None of them opens a network connection, calls the cloud, or screens anything:

Path	What it is	Network
README.md, NOTICE, LICENSE	Package provenance and licensing	none
references/architecture.md	Search and evidence-collection rules	none
references/evidence-package-schema.md	The per-paper Evidence Record shape handed to the cloud	none
references/metadata-validation-gate.md	The bibliographic-identity check run before handoff	none
agents/openai.yaml	Descriptor metadata for platforms that read one	none
scripts/check_evidence.py	Local pre-flight: validates one Evidence Record's JSON and fields before pasting	none
scripts/validate_results.py	Local audit of returned results: merges the per-paper rows, checks the product contract	none
scripts/render_excel.py	Local renderer: writes the Excel Paper Sheet and Reading List	none

Searching, evidence collection, the metadata gate, workbook filling, and cloud submission are performed by the agent using its own tools plus the loomloom CLI declared in this skill's frontmatter. They are not implemented in the bundled scripts.

Files these scripts read and write. Read: the cloud result export passed to --input (result-rows.json) and, for the pre-flight checker, one Evidence Record JSON. Written: the audit outputs review/local-audit.json and review/validation-report.json, plus the deliverables PaperSheet.xlsx and ReadingList.xlsx under --out-dir. Nothing else is read or written, no network request is made, and any other path is out of scope for this skill.

Before you start: pick language & payment channel

1. Cloud output language — confirm it with the user. The package only sets the default: this is the English package, so the default is English; the -zh package is the Simplified-Chinese counterpart. Ask the user which language they want for the delivered comments and summaries before the run. If the assignment requires another language, keep this package and write those fields in the required language (see the language rule in step 5); if the user wants a Chinese default throughout, point them at the -zh package.
2. Which Cloud to pay (run cost is charged where you execute):
   • Domestic / RMB: Shengsuanyun, CNY 0.7 / task
   • Overseas / USD: CogFoundry, USD 0.10 / task
3. Input is required. The cloud has NO internet; it evaluates ONLY the evidence text you paste. No input, no output.
4. Full local packages (scripts/references/agents; -zh and -en) live on GitHub: https://github.com/ez-hq/literature-review-paper-screener/releases

Workflow

1. Install/verify LoomLoom

bash

loomloom doctor --output json

If healthy=false, complete authentication first (browser login preferred: loomloom login; fallback API token in the platform console). Do not proceed to cloud steps without a healthy Doctor.

1.5 Ask the user which Cloud platform to run on

The SkillBot is published on two platforms. You must ask the user before any cloud run which platform to use — never decide on their behalf. Payment method is the decision guide:

Platform	Profile	Evidence input mode	Market fee	When to pick
CogFoundry	cogfoundry	Paste the single-paper record JSON into the cell (v2 platform: upload port removed)	USD 0.10 / task	Credit-card / international payment (USD) — English output
ShengSuanYun	shengsuanyun	Paste the single-paper record JSON into the cell (no upload port on v2)	CNY 0.70 / task	China payment (WeChat/Alipay/RMB) — Chinese-language listing; outputs in Simplified Chinese

Ask in plain language, e.g.: "Which platform should I run on? CogFoundry (USD — credit card, English output) or ShengSuanYun (CNY — Chinese output)?"

Then switch the active profile and verify health before proceeding:

bash

loomloom server list
loomloom server use <cogfoundry|shengsuanyun>
loomloom doctor --output json

The screening logic is identical; only the evidence-entry mechanics and fee differ. The platform choice is confirmed again at submission time (step 8) together with the cost — if the user changes platform after evidence entry, redo the platform-specific evidence-entry step (6) for the new platform.

2. Understand your template binding

This Skill orchestrates a private template version on each platform. Current bindings (do not invent IDs):

Platform	Template ID	Version ID
CogFoundry	76484632-796a-4980-bfc5-180c9fd4200f	271f17cf-566f-41fd-80fa-3985a59df62c (v1.5, v2 syntax, paste mode, English-only)
ShengSuanYun	a9e2cf68-e1c5-4b01-ab40-85dc6d44d893	b394726b-6e18-429c-a9c0-53daf6f3c2eb (v7, Chinese-only)

Verify with loomloom template-spec get <template-id> before running. If the binding changes, ask the owner; never guess IDs.

3. Gather user input (conversational)

Ask, one question at a time, in plain language (all optional except the topic):

1. Research Question / Topic — required
2. Required Citation Count — optional (guidance only)
3. Assignment Requirements (brief, rubric, word count, population, etc.) — optional
4. Research Restrictions (population, country/region, time period, source type, years) — optional
5. Deadline — optional (reading recommendation only)
6. Available Reading Time — optional

Never block on missing optional inputs; skipped fields use default rules. If the topic is too unclear, ask one clarification question, then proceed with what you have.

4. Search the literature (you, local, internet-enabled)

Per the search workflow rules (see references/architecture.md):

• Build a search profile from available input; never invent restrictions the user did not provide.
• Decompose the question into core concepts, research focus, population, context.
• Build a keyword map (synonyms, alternative terminology, academic terms).
• Generate multiple search queries (direct, relationship, terminology expansion, population/context).
• Run them; maximize recall; do NOT screen for quality during search.
• Run a coverage check (all core concepts, synonyms, population, context, direct evidence, alternative perspectives, foundational + recent research). Expand only when new searches still add new literature; stop when new searches produce mainly duplicates/covered/low-relevance.
• Combine everything into a Master Candidate Pool, then deduplicate (DOI, accession, title) into the Unique Candidate Pool.

5. Collect evidence and build one Evidence Record per paper

For every unique candidate, collect as much as is reasonably available:

• Bibliographic metadata (title, authors, year, journal/publisher, source type, DOI, ISBN, stable URL, database record)
• Abstract
• Available content: full text where possible; otherwise sections (intro/methods/results/discussion/conclusion) or structured info (methods info, key findings, results info, conclusion info, database record detail)
• Stable links (paper link, DOI link, database record, publisher page)

Then assign one Evidence Availability Level per paper:

Level	Record contains
A	Full text, or substantial full-paper content (Methods, Results, Discussion, Conclusion)
B	Abstract + substantial structured information (methods info, key findings, results, conclusions, detailed database record)
C	Title + metadata + Abstract
D	Title, authors, year, journal/publisher only

Record per paper: Available Evidence, Missing Evidence, Assessment Limitations. Do not fabricate evidence; do not require full text for every paper; failed retrieval only lowers the level.

Output = one standalone JSON/text file per paper (the per-paper Evidence Record, see references/evidence-package-schema.md for the exact shape), named like handoff_p001.json… handoff_pNNN.json. One file must contain exactly one paper's record — this is what keeps a single cloud task small enough to finish inside the platform activity timeout. Do not bundle all papers into one file.

Language rule: the Evidence Record defaults to English.

• Default. English is the default for every field the local agent writes: available_content, available_evidence, missing_evidence, assessment_limitations, abstract_or_available_content, metadata_gate_notes, and any notes. The default comes from the cloud template bound to this package, which is configured for English output, so English input keeps the cloud summary/notes, Paper Sheet, and Reading List consistent end-to-end.
• Override. Assignment requirements take precedence over the default. If the user's assignment requires the delivered comments and summaries in another language, write those fields in that language and say so in the handoff notes. If the user simply asks for a different output language, honour the request and record which language was used.
• Literature content (abstract, full-text excerpts, structured info) is never translated: keep the paper's original language as-is (keep an English paper's English).
• Want a different package default? The -zh package is the Simplified-Chinese counterpart of this one, and installing it makes Chinese the package default.

5.5 Metadata Validation Gate (mandatory, before handoff)

Before any per-paper record may be written into its handoff_p<record_id>.json, run the Metadata Validation Gate (see references/metadata-validation-gate.md) against authoritative sources (PubMed / Crossref). This gate validates bibliographic identity only — it never touches search logic, screening logic, CRAAP, Topic Relevance, Reading Role, Priority, the Cloud DAG, or workbook batching.

• Every unique candidate receives exactly one outcome: VERIFIED | PARTIALLY VERIFIED | MISMATCH | INVALID.
• VERIFIED / PARTIALLY VERIFIED → record may proceed; write "metadata_status": "VERIFIED"|"PARTIALLY VERIFIED" into the handoff record and mark any unverifiable identifier explicitly ("doi": "NOT VERIFIED").
• MISMATCH / INVALID → the record is blocked before handoff_p<record_id>.json, cloud upload, screening, and final delivery. Return it to evidence collection (step 5) for re-verification; never guess, infer, or repair identity with semantic similarity. If re-verification cannot resolve identity, surface the conflicting values to the owner and let the owner decide keep/drop.
• No DOI/PMID and no authoritative confirmation (not indexed by PubMed/Crossref): keep the record as PARTIALLY VERIFIED with identifiers marked NOT VERIFIED — never silently drop valid literature; flag it in the gate ledger and delivery summary for owner awareness.
• Keep a short per-run gate ledger (record_id → status → what was checked) for the delivery summary.
• Core principle: a correct summary does not prove that the citation metadata is correct. Evidence content and bibliographic identity are validated separately.

Optional pre-flight: run python3 scripts/check_evidence.py <evidence.json> before pasting to catch JSON/field errors locally (no cloud, no cost).

5.6 What leaves your machine — cloud handoff, privacy, and data minimization

Steps 1–5.5 (search, evidence collection, the metadata gate, the pre-flight check) run entirely on this machine. The handoff at step 6 is the first and only place where data leaves it. Before you paste or upload anything:

1. Disclose before you send. Tell the user, in plain language, which platform will receive the data, that it is a third-party cloud service, and what the run will cost. A confirmation about platform and fee alone is not consent to transfer data — ask for the data transfer explicitly.
2. Minimize what you send. Send only what screening needs: the per-paper Evidence Record fields defined in references/evidence-package-schema.md. Strip anything else from the payload — student names, student numbers, email addresses, phone numbers, home addresses, ID numbers, grades, and any other personal or identifying detail. If the research question or the assignment brief itself contains such detail, replace it with a neutral placeholder before it reaches the cloud and tell the user you did so.
3. Local alternative. Everything up to and including the Evidence Records, the metadata gate ledger, and the pre-flight check is local and free. If the user does not consent to sending data to a third-party cloud, stop here and deliver the local artifacts (per-paper Evidence Records plus the gate ledger), stating plainly that no cloud screening was run and therefore no Paper Sheet or Reading List was produced. Never send the data anyway, and never substitute a local guess for a screening result.
4. No credentials in the payload. Never include API tokens, keys, or account identifiers in any handoff payload.

6. Prepare the cloud workbook (one row per paper)

Download the workbook for the exact version:

bash

loomloom template-spec download-workbook 76484632-796a-4980-bfc5-180c9fd4200f 271f17cf-566f-41fd-80fa-3985a59df62c

Fill one row per paper (N papers → N rows):

• Research Question / Topic — the same required topic text on every row

• Assignment Requirements, Research Restrictions — optional; same values on every row when provided

• Required Citation Count, Deadline, Available Reading Time — optional (collected for context only)

• Screening Model — select from the approved list once; leave default if fine

• Literature Evidence Package — platform-dependent:

  • CogFoundry: upload each per-paper record as its own text/plain asset and put that row's input_asset_id in the cell:

    bash

    # one upload per paper
    loomloom input-asset upload handoff_p001.json
    # -> asset id for row 1
    loomloom input-asset upload handoff_p002.json
    # -> asset id for row 2  ... and so on
    

  • ShengSuanYun: its v2 TemplateSpec exposes no text-upload port, so paste the per-paper record as compact single-line JSON (see references/evidence-package-schema.md) directly into the cell. Keep it under ~25,000 chars per cell (Excel cell limit is 32,767).

Every row's evidence must reference a different single-paper record (a separate asset on CogFoundry, a separate pasted record on ShengSuanYun). Reusing one multi-paper bundle on every row is forbidden (it reintroduces the timeout).

7. Validate and precheck (read-only)

bash

loomloom template-spec validate-workbook <template-id> <version-id> <filled.xlsx>
loomloom template-spec precheck-workbook <template-id> <version-id> <filled.xlsx>

Show the owner, before any submission:

• task count = paper count N (rows in the workbook)
• per-task fee (Market: USD 0.10) and total fee = 0.10 × N (private-template precheck reports model cost only — state both clearly)
• estimated model/API cost from the precheck, plus balance and sufficiency

Do not submit yet.

8. Confirmed run (platform + fee + count lock)

Before anything else, re-confirm the platform with the owner (even if chosen in step 1.5):

• ShengSuanYun — CNY ¥0.70/task, China payment (WeChat/Alipay/RMB)
• CogFoundry — USD $0.10/task, credit-card payment

Then present the full numbers and get an explicit confirmation, phrased as: "Platform: . N papers → N cloud tasks → total fee ≈ <0.70 CNY × N | 0.10 USD × N> + model cost. Confirm?" The row count is the paper-count lock: the number of tasks (and fee units) is fixed before submission and cannot change mid-run. Also verify the active profile matches the confirmed platform (loomloom doctor). If the owner changes platform at this point, go back to step 6 (evidence entry) for the new platform. Then:

bash

loomloom template-spec submit-workbook <template-id> <version-id> <filled.xlsx> --client-request-id <new-uuid>

Preserve the returned run_id. Watch and retrieve all task results:

bash

loomloom run watch <run-id>
loomloom run result-rows <run-id> --output result-rows.json
loomloom run result-workbook <run-id> --output-file results.xlsx

Every run needs its own confirmation and its own client-request-id. If input changes after confirmation, re-validate, re-precheck, show a new estimate, and obtain a new confirmation.

9. Local audit (mandatory — merged)

Run the validator on the returned results (it merges all per-paper task outputs into one global screened pool automatically):

bash

python3 scripts/validate_results.py --input result-rows.json --manifest ../store-manifest.json --out-dir ../review

It must PASS before you render or claim success. The validator checks: parseable structured output for every task row, evidence availability levels, content-credibility decision rule, excluded papers never in the Paper Sheet, same pool across Paper Sheet and Reading List, one Primary Reading Role per paper, no duplicate record IDs across batches, citations present, explicit failures/partial results, and reproducible rerun conditions. If it reports issues, do not fabricate fixes — record them and report to the owner.

10. Render and deliver (merged)

Run the Excel renderer over the audited result set (it merges every task row's output into one Paper Sheet + one Reading List):

bash

python3 scripts/render_excel.py --input result-rows.json --out-dir <deliverables>

Deliver: Paper Sheet (complete screened pool, one row per retained paper) + Reading List (same pool by Priority and Reading Role) as Excel files, plus a short plain-language summary: how many papers searched, screened, included, excluded (with reasons), the evidence-level breakdown (A/B/C/D), and how many cloud tasks ran. Point out evidence-limited papers (Levels C/D) and preliminary classifications.

Before delivery, verify the outputs are in the agreed language (English by default, or the assignment-required language when one was specified) — scan the rendered data and the handoff for text in a different language; if any is found, return to step 5 (evidence collection), rewrite the offending fields, and re-run the affected stages:

bash

# quick check: prints any records containing CJK characters in the rendered output
python3 -c "
import sys, json, re
for f in sys.argv[1:]:
    d = json.load(open(f, encoding='utf-8'))
    hits = [k for k, v in (d.items() if isinstance(d, dict) else []) if isinstance(v, str) and re.search(r'[\u4e00-\u9fff]', v)]
    print(f, 'CJK fields:', hits if hits else 'none')
" result-rows.json handoff_p*.json

Operating rules

• Ask the user which platform before every cloud run — including test and verification runs. Never default to the currently active profile without asking (step 1.5), and never skip the platform + fee + count confirmation ceremony (step 8) for any run, test or not. The confirmation must come from the user after the numbers have been shown: silence, a previous run's approval, or an earlier platform choice is not a confirmation, and if the user does not respond you do not submit. A run that spends money without asking is a rule violation, not an internal shortcut.
• Handoff content and delivered outputs follow the language rule in step 5 (English by default, or the assignment-required language when one was specified). Literature content always keeps its original language — cite a paper in the language it was published in, and never translate article content. Do not let the conversation language silently change the language of the record: if it differs from the agreed output language, say so before continuing.
• One paper per workbook row / per cloud task. Never bundle multiple papers into one evidence asset or one row; multi-paper single rows time out on the platform (V1.1 fixes this by design). If a row's task fails or times out, retry that row alone — do not "merge" papers to retry.
• The Cloud has no internet: it evaluates only the evidence you send. Never ask it to search, fetch, or open URLs, and never claim it reviewed full text you did not provide.
• Evidence Availability ≠ Quality. A Level C/D paper is not lower quality; its assessment is shallower and must be flagged, not dropped.
• Search broadly. Screen carefully. Keep all qualified literature. Deadline / reading time / citation count recommend what to read first — they never remove literature from the outputs.
• Never include excluded papers in the Paper Sheet or Reading List.
• Never expose the LoomLoom token, raw user data, or the contents of the private cloud template.
• If the LoomLoom dependency is missing or Doctor is unhealthy, stop cloud stages and report BLOCKED — do not invent commands or remotely create state.