refren 0.1.0__py3-none-any.whl

refren-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: refren
+Version: 0.1.0
+Summary: Scientific manuscript PDF file renamer
+License: MIT
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: anthropic>=0.86.0
+Requires-Dist: pdfplumber>=0.11
+Description-Content-Type: text/markdown
+
+# refren: scientific manuscript PDF file renamer
+
+```bash
+$ ./refren.py 1758-2946-6-10.pdf 
+  (direct parsing incomplete — calling Claude API...)
+  First author last name : Krstajic
+  Second author last name: Buturovic
+  Journal                : Journal of Cheminformatics -> J Cheminform
+  Year                   : 2014
+
+  1758-2946-6-10.pdf  ->  Krstajic_Buturovic_JCheminform_2014.pdf
+Rename? [y/N] y
+Renamed to: Krstajic_Buturovic_JCheminform_2014.pdf
+```
+

refren-0.1.0.dist-info/RECORD

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+refren.py,sha256=jqJe8l2Qdjz0fcKWQwyxeHpUyda_cvZggJdgot6ta8A,8461
+refren-0.1.0.dist-info/METADATA,sha256=qU5yYrlaxr1Es_9To5YFu7Nd5I-v2cHAh5YQZBfg8OY,726
+refren-0.1.0.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+refren-0.1.0.dist-info/entry_points.txt,sha256=MkoRFSweBva1PR16nAHJV12blb97lxLbF1KZ4UTqIfg,39
+refren-0.1.0.dist-info/licenses/LICENSE,sha256=KFDwGS4OaI3VKJPFDHSmj8CakM5sD6WPDJN0_FN4MEQ,1068
+refren-0.1.0.dist-info/RECORD,,

refren-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.29.0
+Root-Is-Purelib: true
+Tag: py3-none-any

refren-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+refren = refren:main

refren-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 ljbuturovic
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

refren.py

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+#!/usr/bin/env python3
+"""
+Rename a scientific PDF as: FirstAuthorLastName_SecondAuthorLastName_JournalAbbrev_Year.pdf
+Usage: ./renamer.py <pdf_file>
+"""
+
+import re
+import sys
+from pathlib import Path
+
+import anthropic
+import pdfplumber
+from pydantic import BaseModel
+
+
+# --- Journal abbreviation lookup ---
+JOURNAL_ABBREVIATIONS = {
+    "diagnostic and prognostic research": "DiagProgRes",
+    "nature medicine": "NatMed",
+    "nature communications": "NatCommun",
+    "nature": "Nature",
+    "science": "Science",
+    "cell": "Cell",
+    "the lancet": "Lancet",
+    "lancet": "Lancet",
+    "new england journal of medicine": "NEJM",
+    "n engl j med": "NEJM",
+    "jama": "JAMA",
+    "bmj": "BMJ",
+    "annals of internal medicine": "AnnInternMed",
+    "plos medicine": "PLoSMed",
+    "plos one": "PLoSOne",
+    "plos biology": "PLoSBiol",
+    "plos computational biology": "PLoSComputBiol",
+    "bioinformatics": "Bioinformatics",
+    "nucleic acids research": "NucleicAcidsRes",
+    "genome biology": "GenomeBiol",
+    "genome research": "GenomeRes",
+    "molecular cell": "MolCell",
+    "cell reports": "CellRep",
+    "cell systems": "CellSyst",
+    "elife": "eLife",
+    "journal of clinical oncology": "JClinOncol",
+    "cancer research": "CancerRes",
+    "cancer cell": "CancerCell",
+    "clinical cancer research": "ClinCancerRes",
+    "journal of the american medical informatics association": "JAMIA",
+    "npj digital medicine": "NPJDigitMed",
+    "artificial intelligence in medicine": "ArtifIntellMed",
+    "medical image analysis": "MedImageAnal",
+    "radiology": "Radiology",
+    "european radiology": "EurRadiol",
+    "circulation": "Circulation",
+    "european heart journal": "EurHeartJ",
+    "journal of the american college of cardiology": "JACC",
+    "diabetes care": "DiabetesCare",
+    "statistics in medicine": "StatMed",
+    "biometrics": "Biometrics",
+    "american journal of epidemiology": "AmJEpidemiol",
+    "epidemiology": "Epidemiology",
+    "international journal of epidemiology": "IntJEpidemiol",
+    "brain": "Brain",
+    "journal of neurology": "JNeurol",
+    "neurology": "Neurology",
+    "gut": "Gut",
+}
+
+
+def abbreviate_journal(full_name: str) -> str:
+    """Return a known abbreviation or derive a CamelCase abbreviation from the title."""
+    lower = full_name.lower().strip()
+    for key, abbr in JOURNAL_ABBREVIATIONS.items():
+        if key in lower:
+            return abbr
+    stop = {"a", "an", "the", "of", "in", "on", "and", "for", "to", "with", "&"}
+    words = re.sub(r"[^\w\s]", "", full_name).split()
+    return "".join(w.capitalize() for w in words if w.lower() not in stop) or "UnknownJournal"
+
+
+def extract_last_name(name: str) -> str:
+    """Return the last name from a full author name string (final word only)."""
+    name = name.strip().rstrip(",*0123456789† ")
+    parts = name.split()
+    return parts[-1] if parts else name
+
+
+def parse_authors_and_year(text: str):
+    """
+    Extract (first_author_last, second_author_last, year) from first-page text.
+    Returns (first, second, year) — any may be None if not found.
+    """
+    year = None
+    year_match = re.search(r"\b(20\d{2}|19\d{2})\b", text)
+    if year_match:
+        year = year_match.group(1)
+
+    first, second = None, None
+
+    # Pattern 1: "Surname et al." header
+    et_al_match = re.search(r"([A-Z][a-z]+(?:\s+[a-z]+)*)\s+et al\.", text)
+    if et_al_match:
+        first = et_al_match.group(1).strip()
+
+    # Pattern 2: full author line — comma-separated "Firstname Lastname, ..."
+    author_line_pattern = re.compile(
+        r"([A-Z][a-z]+(?:\s+[a-z]+)*\s+[A-Z][a-zA-Z\-]+[0-9†*,]*"
+        r"(?:\s*,\s*[A-Z][a-z]+(?:\s+[a-z]+)*\s+[A-Z][a-zA-Z\-]+[0-9†*,]*){1,})"
+    )
+    for match in author_line_pattern.finditer(text):
+        candidate = match.group(0)
+        raw_authors = [a.strip() for a in re.split(r",\s*", candidate) if a.strip()]
+        if len(raw_authors) >= 2:
+            last_names = [extract_last_name(a) for a in raw_authors]
+            if not first:
+                first = last_names[0]
+            second = last_names[1]
+            break
+
+    return first, second, year
+
+
+def extract_journal(text: str) -> str | None:
+    """Try to find the journal name from the first-page text."""
+    lower = text.lower()
+    for key in JOURNAL_ABBREVIATIONS:
+        if key in lower:
+            idx = lower.find(key)
+            return text[idx: idx + len(key)]
+    patterns = [
+        r"(?:published in|journal)[:\s]+([A-Z][^\n]+)",
+        r"https?://doi\.org/[^\s]+\s+([A-Z][A-Za-z &]+)\n",
+    ]
+    for pat in patterns:
+        m = re.search(pat, text, re.IGNORECASE)
+        if m:
+            return m.group(1).strip()
+    return None
+
+
+def sanitize(s: str) -> str:
+    """Remove characters unsafe for filenames."""
+    return re.sub(r"[^\w]", "", s)
+
+
+# --- Claude API fallback ---
+
+class PaperMetadata(BaseModel):
+    first_author_last_name: str
+    second_author_last_name: str
+    journal_full_name: str
+    journal_abbreviation: str
+    year: str
+
+
+def extract_via_llm(text: str, metadata: dict | None = None) -> PaperMetadata:
+    """Use Claude to extract paper metadata from first-page text."""
+    print("  (direct parsing incomplete — calling Claude API...)")
+    client = anthropic.Anthropic()
+    response = client.messages.parse(
+        model="claude-opus-4-6",
+        max_tokens=512,
+        system=(
+            "You are a scientific literature assistant. "
+            "Extract bibliographic metadata from the first page of a scientific paper. "
+            "For journal_abbreviation, use the standard ISO/NLM abbreviation (e.g. 'Circulation', "
+            "'N Engl J Med', 'JAMA', 'Nat Med'). "
+            "Return only last names for authors (no initials, no titles, no credentials)."
+        ),
+        messages=[{
+            "role": "user",
+            "content": (
+                "Extract the metadata from this scientific paper.\n\n"
+                + (f"PDF metadata: {metadata}\n\n" if metadata else "")
+                + f"First page text:\n{text[:4000]}"
+            ),
+        }],
+        output_format=PaperMetadata,
+    )
+    return response.parsed_output
+
+
+def rename_pdf(pdf_path: str):
+    path = Path(pdf_path)
+    if not path.exists():
+        print(f"Error: file not found: {pdf_path}")
+        sys.exit(1)
+    if path.suffix.lower() != ".pdf":
+        print(f"Error: not a PDF file: {pdf_path}")
+        sys.exit(1)
+
+    with pdfplumber.open(path) as pdf:
+        metadata = pdf.metadata or {}
+        first_page_text = pdf.pages[0].extract_text() or ""
+        if len(first_page_text) < 200 and len(pdf.pages) > 1:
+            first_page_text += "\n" + (pdf.pages[1].extract_text() or "")
+
+    first, second, year = parse_authors_and_year(first_page_text)
+    journal_full = extract_journal(first_page_text)
+    journal_abbr = abbreviate_journal(journal_full) if journal_full else None
+
+    # Try to extract year from PDF metadata if not found in text
+    if not year:
+        meta_str = " ".join(str(v) for v in metadata.values())
+        m = re.search(r"\b(20\d{2}|19\d{2})\b", meta_str)
+        if m:
+            year = m.group(1)
+
+    missing = [label for label, val in [
+        ("first author", first), ("second author", second),
+        ("year", year), ("journal", journal_full),
+    ] if not val]
+
+    if missing:
+        # When LLM is needed, trust it for all fields — regex results may also be wrong
+        meta = extract_via_llm(first_page_text, metadata)
+        first = meta.first_author_last_name
+        second = meta.second_author_last_name
+        year = meta.year
+        journal_full = meta.journal_full_name
+        journal_abbr = meta.journal_abbreviation
+
+    print(f"  First author last name : {first}")
+    print(f"  Second author last name: {second}")
+    print(f"  Journal                : {journal_full} -> {journal_abbr}")
+    print(f"  Year                   : {year}")
+
+    new_name = f"{sanitize(first)}_{sanitize(second)}_{sanitize(journal_abbr)}_{sanitize(year)}.pdf"
+    new_path = path.parent / new_name
+
+    print(f"\n  {path.name}  ->  {new_name}")
+    confirm = input("Rename? [y/N] ").strip().lower()
+    if confirm == "y":
+        path.rename(new_path)
+        print(f"Renamed to: {new_path}")
+    else:
+        print("Aborted.")
+
+
+def main():
+    if len(sys.argv) != 2:
+        print("Usage: ./renamer.py <pdf_file>")
+        sys.exit(1)
+    rename_pdf(sys.argv[1])
+
+
+if __name__ == "__main__":
+    main()