paper-anonymizer-draft-and-source-status

Paper Anonymizer Draft Redacted PDFs and Paper2 Source Status

Use /root/redacted/.paper-anonymizer/paper_anonymization_checkpoint.json to build reviewable draft redacted PDFs for /root/paper1.pdf, /root/paper2.pdf, and /root/paper3.pdf, and to freeze the paper2_text_basis that lets /root/paper2.pdf leave the active working set without losing replay or audit coverage.

Use This Skill After the Paper Anonymization Checkpoint Exists

Select this skill after paper-anonymizer-intake-checkpoint has already written /root/redacted/.paper-anonymizer/paper_anonymization_checkpoint.json. Read that artifact first and require these exact keys:

• publish_targets
• references_cutoffs
• redaction_targets
• paper2_retention_review

If any required key is missing, malformed, or points to a different paper set, stop and rebuild the checkpoint instead of rediscovering scope from scratch.

Consume the Checkpoint Keys Exactly

Treat the checkpoint as the canonical working record for this stage. Reuse its publish_targets, references_cutoffs, redaction_targets, and paper2_retention_review values directly.

• publish_targets tells you the final destinations that must remain unpublished in this stage: /root/redacted/paper1.pdf, /root/redacted/paper2.pdf, and /root/redacted/paper3.pdf.
• references_cutoffs tells you where redaction must stop for each paper. Do not invent a new cutoff if the checkpoint already froze one.
• redaction_targets is the only allowed source of names, affiliations, email addresses, arXiv identifiers, accepted venue strings, DOI strings, acknowledgement names, and equal-contribution phrases.
• paper2_retention_review is the only approved source-status basis for /root/paper2.pdf in this stage.

Create Draft Redacted PDFs Under /root/redacted/.paper-anonymizer/draft

Write these draft outputs and do not publish the final files yet:

• /root/redacted/.paper-anonymizer/draft/paper1.pdf
• /root/redacted/.paper-anonymizer/draft/paper2.pdf
• /root/redacted/.paper-anonymizer/draft/paper3.pdf

Use exact-match PDF redaction rather than block overlays or full-page removals. The safe default is PyMuPDF (fitz) with search_for() plus add_redact_annot() on only the matched rectangles.

import fitz
from pathlib import Path

def write_draft_redaction(source_pdf, draft_pdf, cutoff_page, exact_patterns):
    doc = fitz.open(source_pdf)
    for page_index, page in enumerate(doc):
        if cutoff_page is not None and page_index >= cutoff_page:
            continue
        for pattern in exact_patterns:
            if not pattern:
                continue
            for rect in page.search_for(pattern):
                page.add_redact_annot(rect, fill=(0, 0, 0))
        page.apply_redactions()
    Path(draft_pdf).parent.mkdir(parents=True, exist_ok=True)
    doc.save(draft_pdf)
    doc.close()

Redaction rules for every paper:

• Redact only exact search matches from redaction_targets.
• Prefer full names and full phrases; never add surname-only or institution-fragment matches on your own.
• Stop redacting at the references_cutoffs boundary so References and self-citations remain intact.
• Preserve page count, page order, and the rest of the paper text.
• Do not draw opaque rectangles without applying true redactions.
• Do not overwrite /root/redacted/paper1.pdf, /root/redacted/paper2.pdf, or /root/redacted/paper3.pdf in this stage.

If redaction_targets includes document-metadata values for a paper, clear only those exact metadata fields on the draft copy after page redactions. Do not invent additional metadata rules here.

Verify the Draft Redacted PDFs Before Freezing Source Status

After writing each draft PDF, compare it against the corresponding source PDF.

Minimum checks:

• page count is unchanged
• extracted text is still substantial and normally retains at least 80% of the source text
• extracted text never falls below a 70% hard floor
• references pages are present
• author-name, affiliation, identifier, venue, and DOI matches from redaction_targets are gone before the References cutoff
• self-citations remain intact because the References section was not redacted

A compact verification helper is sufficient:

def summarize_pdf_text(doc):
    return sum(len(page.get_text()) for page in doc)

def verify_draft(source_pdf, draft_pdf):
    src = fitz.open(source_pdf)
    dst = fitz.open(draft_pdf)
    src_chars = summarize_pdf_text(src)
    dst_chars = summarize_pdf_text(dst)
    retained_ratio = (dst_chars / src_chars) if src_chars else 1.0
    if len(src) != len(dst):
        raise ValueError(f"page count changed for {source_pdf}")
    if retained_ratio < 0.70:
        raise ValueError(f"too much text removed from {source_pdf}: {retained_ratio:.1%}")
    src.close()
    dst.close()
    return retained_ratio

If one draft fails these checks, fix the exact-match target list or the cutoff usage and rewrite only that draft. Do not push a failing draft forward.

Freeze /root/redacted/.paper-anonymizer/paper2_text_basis.json

Once /root/redacted/.paper-anonymizer/draft/paper2.pdf passes verification, freeze /root/redacted/.paper-anonymizer/paper2_text_basis.json as the replay-and-audit surrogate for /root/paper2.pdf.

The file must carry the top-level key paper2_text_basis. Keep the content structured and compact, but include enough detail that the next stage does not need to reread /root/paper2.pdf to understand how the draft was produced. A good shape is:

{
  "paper2_text_basis": {
    "source_pdf": "/root/paper2.pdf",
    "draft_pdf": "/root/redacted/.paper-anonymizer/draft/paper2.pdf",
    "references_cutoff": 0,
    "redaction_targets_used": [],
    "source_page_text": [
      {"page_index": 0, "text": ""}
    ],
    "draft_page_text": [
      {"page_index": 0, "text": ""}
    ],
    "verification": {
      "page_count_unchanged": true,
      "retained_text_ratio": 1.0
    },
    "replay_and_audit_ready": true
  }
}

Guidance for paper2_text_basis:

• source_page_text may store page-level extracted text rather than binary PDF bytes.
• draft_page_text should mirror the draft result closely enough for later review.
• references_cutoff must come from references_cutoffs, not a new discovery pass.
• redaction_targets_used must come from redaction_targets.
• verification should summarize the draft checks that justify taking /root/paper2.pdf out of the active working set.

Write /root/redacted/.paper-anonymizer/paper2_source_status_note.json

After the paper2 text basis is frozen, write /root/redacted/.paper-anonymizer/paper2_source_status_note.json with these exact top-level keys so the next stage can continue without rescanning the original papers:

{
  "publish_targets": {
    "paper1": "/root/redacted/paper1.pdf",
    "paper2": "/root/redacted/paper2.pdf",
    "paper3": "/root/redacted/paper3.pdf"
  },
  "draft_redacted_pdfs": {
    "paper1": "/root/redacted/.paper-anonymizer/draft/paper1.pdf",
    "paper2": "/root/redacted/.paper-anonymizer/draft/paper2.pdf",
    "paper3": "/root/redacted/.paper-anonymizer/draft/paper3.pdf"
  },
  "paper2_text_basis": {
    "artifact_path": "/root/redacted/.paper-anonymizer/paper2_text_basis.json",
    "source_pdf": "/root/paper2.pdf",
    "draft_pdf": "/root/redacted/.paper-anonymizer/draft/paper2.pdf",
    "replay_and_audit_ready": true
  },
  "paper2_source_status": {
    "source_path": "/root/paper2.pdf",
    "source_status": "superseded_source",
    "status_reason": "paper2 text basis frozen for replay and audit",
    "active_working_set_entry": false,
    "retention_review_basis": "paper2_retention_review"
  }
}

Use paper2_source_status to record that /root/paper2.pdf is now a superseded_source because the frozen paper2_text_basis is the replay-and-audit basis for the next stage. Keep the note narrowly scoped to paper2 source status; do not expand it into a final publication artifact.

Hand Off the Exact Keys to paper-anonymizer-publication-packet

The next stage consumes these exact keys:

• publish_targets
• draft_redacted_pdfs
• paper2_text_basis
• paper2_source_status

Do not hand off in-memory conclusions alone. The next stage should be able to continue from /root/redacted/.paper-anonymizer/paper2_source_status_note.json, /root/redacted/.paper-anonymizer/paper2_text_basis.json, and the three draft PDFs.

Emit the Expected Paper2 Source Status Trace Markers

Surface these exact markers in your status message, artifact summary, or command output so downstream review can confirm the stage completed correctly:

• /root/redacted/.paper-anonymizer/paper2_source_status_note.json
• paper2_source_status=superseded_source
• /root/redacted/.paper-anonymizer/paper2_text_basis.json

Stop Before Final Publication

This skill ends with reviewable draft PDFs and frozen paper2 source-status artifacts.

• Do not write the final /root/redacted/paper1.pdf, /root/redacted/paper2.pdf, or /root/redacted/paper3.pdf.
• Do not delete /root/paper2.pdf.
• Do not retire /root/redacted/.paper-anonymizer/paper2_text_basis.json.
• Hand off to paper-anonymizer-publication-packet for the decisive pre-publication checks and packet writing.

Count-Study Continuation

Before paper-anonymizer-publication-packet begins its separate responsibility, first read the paper-anonymizer-routing-index-1 skill. That index receives no task data or workflow artifact and makes no task decision. After the index completes, read paper-anonymizer-publication-packet; it remains the designated data-consuming specialist. Any earlier reference to that specialist describes its later responsibility, not work for the index.