odysseus/src/personal_docs.py at dev · odysseus-dev/odysseus · GitHub

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# src/personal_docs.py

import os

import re

import json

import logging

from typing import List, Dict, Set, Any, Tuple

from dataclasses import dataclass

from src.index_walk import prune_index_dirs, is_indexable_file

from src.markitdown_runtime import MARKITDOWN_EXTS

logger = logging.getLogger(__name__)

def extract_pdf_text(file_path: str) -> str:

"""Extract text from a PDF file using pypdf (permissive, BSD)."""

try:

from pypdf import PdfReader

reader = PdfReader(file_path)

text = "".join((page.extract_text() or "") for page in reader.pages)

return text

except ImportError:

logger.warning("pypdf not installed, cannot extract PDF text")

return ""

except Exception as e:

logger.error(f"Failed to extract PDF text from {file_path}: {e}")

return ""

def extract_office_text(file_path: str) -> str:

"""Extract text from an Office/EPUB doc via the optional markitdown dep.

Returns "" when markitdown is missing or extraction fails, mirroring

extract_pdf_text — the indexer then simply skips the file's content.

"""

if file_path.lower().endswith(".doc"):

from src.document_processor import _process_legacy_word_document

return _process_legacy_word_document(file_path, os.path.basename(file_path))

from src.markitdown_runtime import convert_to_markdown

return convert_to_markdown(file_path) or ""

@dataclass

class PersonalDocsConfig:

"""Configuration for personal documents management."""

CHUNK_SIZE: int = 1000

CHUNK_OVERLAP: int = 200

DEFAULT_EXTENSIONS: Tuple[str, ...] = (

".txt", ".md", ".json", ".pdf", ".doc", ".docx", ".pptx", ".xlsx", ".xls", ".epub",

)

DEFAULT_K: int = 5

STOP_WORDS: Set[str] = None

def __post_init__(self):

if self.STOP_WORDS is None:

self.STOP_WORDS = set("""

the a an is are was were be been being to of in for on at by with from

and or if then else when while as it this that those these i you he she

we they my your our their me him her us them

""".split())

# Initialize configuration

config = PersonalDocsConfig()

def read_text_file(path: str) -> str:

"""Read a text file with error handling."""

try:

with open(path, "r", encoding="utf-8", errors="ignore") as f:

return f.read()

except Exception:

return ""

def split_chunks(text: str, size: int = config.CHUNK_SIZE, overlap: int = config.CHUNK_OVERLAP) -> List[str]:

"""Split text into overlapping chunks."""

if not isinstance(text, str):

return []

text = text.strip()

if not text:

return []

chunks = []

i = 0

n = len(text)

while i < n:

j = min(i + size, n)

chunks.append(text[i:j])

if j >= n:

# Reached the end. Without this, the next start (j - overlap) is

# still > i, so the loop appended one extra chunk duplicating the

# last `overlap` chars of the text.

break

i = j - overlap if j - overlap > i else j

return chunks

def tokenize(s: str) -> Set[str]:

"""Tokenize string into words, excluding stop words."""

text = s if isinstance(s, str) else ""

tokens = re.findall(r"[A-Za-z0-9_\-]+", text.lower())

return set(t for t in tokens if t not in config.STOP_WORDS and len(t) > 1)

def load_personal_index(

personal_dir: str,

extensions: Tuple[str, ...] = config.DEFAULT_EXTENSIONS

) -> List[Dict[str, Any]]:

"""Load and index personal documents.

Skips hidden and junk directories and hidden files via the shared

``index_walk`` policy, so the keyword index matches the vector index and a

real vault/repo does not sweep in ``.obsidian/`` / ``.git/`` /

``node_modules/`` content (#5559).

"""

files = []

for root, dirs, names in os.walk(personal_dir):

prune_index_dirs(dirs)

for name in sorted(names):

if not is_indexable_file(name):

continue

p = os.path.join(root, name)

if not os.path.isfile(p):

continue

if not any(name.lower().endswith(ext) for ext in extensions):

continue

size = os.path.getsize(p)

ext = os.path.splitext(name)[1].lower()

if ext == ".pdf":

text = extract_pdf_text(p)

elif ext == ".doc" or ext in MARKITDOWN_EXTS:

text = extract_office_text(p)

else:

text = read_text_file(p)

chunks = split_chunks(text)

display = os.path.relpath(p, personal_dir)

files.append({"name": display, "path": p, "size": size, "chunks": chunks})

return files

def retrieve_personal_keyword(personal_index: List[Dict], query: str, k: int = 5) -> List[str]:

"""

Retrieve relevant documents using keyword search.

Args:

personal_index: The loaded document index

query: Search query

k: Number of results to return

Returns:

List of formatted search results

"""

q = tokenize(query)

if not q:

return []

scored = []

for f in personal_index:

if not isinstance(f, dict):

continue

for idx, ch in enumerate(f.get("chunks") or []):

score = len(q & tokenize(ch))

if score > 0:

scored.append((score, f.get("name", ""), idx, ch))

scored.sort(key=lambda x: x[0], reverse=True)

out = []

for s, fname, idx, ch in scored[:k]:

out.append(f"[{fname} :: chunk {idx+1}]\n{ch}")

return out

def retrieve_personal(personal_index: List[Dict], query: str, k: int = 5,

rag_manager=None) -> List[str]:

"""

Retrieve relevant personal documents using vector search first, falling back to keyword search.

Args:

personal_index: The loaded document index

query: The search query

k: Number of results to return

rag_manager: Optional RAGManager instance for vector search

Returns:

List of formatted search results

"""

if not query:

return []

# First try vector search if RAGManager is available

if rag_manager:

try:

vector_results = rag_manager.search(query, k)

if vector_results:

# Format vector results

out = []

for result in vector_results:

# Extract filename from path

source = result["metadata"].get("source", "")

filename = os.path.basename(source)

# Format the result

formatted = f"[{filename} :: vector search]\n{result['document']}"

out.append(formatted)

return out

except Exception as e:

logger.warning(f"Vector search failed, falling back to keyword search: {e}")

# Fall back to keyword search

return retrieve_personal_keyword(personal_index, query, k)

def _string_list(values) -> list[str]:

return [value for value in values or [] if isinstance(value, str)]

class PersonalDocsManager:

"""Manager class for personal document indexing and retrieval."""

def __init__(self, personal_dir: str, rag_manager=None):

self.personal_dir = personal_dir

self.rag_manager = rag_manager

self.index = []

self.indexed_directories = [] # Track additional directories

self.excluded_files: Set[str] = set() # Files removed from RAG listing

self.directories_file = os.path.join(personal_dir, "indexed_directories.json")

self._excluded_file = os.path.join(personal_dir, "excluded_files.json")

self.load_directories()

self._load_excluded()

self.refresh_index()

def load_directories(self):

"""Load the list of indexed directories from persistent storage."""

try:

if os.path.exists(self.directories_file):

with open(self.directories_file, 'r', encoding="utf-8") as f:

directories = json.load(f)

if not isinstance(directories, list):

raise ValueError("indexed directories must be a list")

self.indexed_directories = _string_list(directories)

logger.info(f"Loaded {len(self.indexed_directories)} indexed directories")

else:

self.indexed_directories = []

except Exception as e:

logger.error(f"Error loading directories: {e}")

self.indexed_directories = []

def save_directories(self):

"""Save the list of indexed directories to persistent storage."""

try:

with open(self.directories_file, 'w', encoding="utf-8") as f:

json.dump(_string_list(self.indexed_directories), f, indent=2)

logger.info(f"Saved {len(self.indexed_directories)} indexed directories")

except Exception as e:

logger.error(f"Error saving directories: {e}")

def _load_excluded(self):

"""Load the set of excluded file paths from persistent storage."""

try:

if os.path.exists(self._excluded_file):

with open(self._excluded_file, 'r', encoding="utf-8") as f:

excluded = json.load(f)

if not isinstance(excluded, list):

raise ValueError("excluded files must be a list")

self.excluded_files = set(_string_list(excluded))

else:

self.excluded_files = set()

except Exception as e:

logger.error(f"Error loading excluded files: {e}")

self.excluded_files = set()

def _save_excluded(self):

try:

with open(self._excluded_file, 'w', encoding="utf-8") as f:

json.dump(_string_list(self.excluded_files), f)

except Exception as e:

logger.error(f"Error saving excluded files: {e}")

def exclude_file(self, filepath: str):

"""Exclude a file from the listing. Persists across restarts."""

self.excluded_files.add(os.path.abspath(filepath))

self._save_excluded()

self.index = [f for f in self.index if os.path.abspath(f.get("path", "")) != os.path.abspath(filepath)]

def add_directory(self, directory: str, *, index: bool = True, owner: str = None):

"""Add a directory to the tracking list and optionally index it."""

# Normalize the path

directory = os.path.abspath(directory)

# Clear any exclusions for files in this directory. Match on a path

# boundary (the directory itself or paths under it) rather than a raw

# string prefix: a bare ``startswith(directory)`` also matches sibling

# directories that merely share a name prefix (e.g. adding ``/docs``

# would wrongly un-exclude files under ``/docs2``).

self.excluded_files = {

p for p in self.excluded_files

if not (p == directory or p.startswith(directory + os.sep))

}

self._save_excluded()

if directory not in self.indexed_directories:

self.indexed_directories.append(directory)

self.save_directories()

logger.info(f"Added directory to tracking: {directory}")

# If RAG manager is available, index the directory immediately.

# Callers that already indexed with owner metadata can pass

# index=False so we do not create a second ownerless copy.

if index and self.rag_manager:

try:

result = self.rag_manager.index_personal_documents(directory, owner=owner)

logger.info(f"Indexed {result.get('indexed_count', 0)} chunks from {directory}")

except Exception as e:

logger.error(f"Failed to index directory {directory}: {e}")

# Refresh the local index to include the new directory

self.refresh_index()

else:

logger.info(f"Directory already indexed: {directory}")

def remove_directory(self, directory: str):

"""Remove a directory from the tracking list."""

# Normalize the path

directory = os.path.abspath(directory)

if directory in self.indexed_directories:

self.indexed_directories.remove(directory)

self.save_directories()

logger.info(f"Removed directory from tracking: {directory}")

# Refresh the index to exclude the removed directory

self.refresh_index()

# Targeted delete of just this directory's chunks. This previously

# called rag_manager.rebuild_index(), which delete+recreates the

# entire shared collection (every owner + the base index) and then

# re-indexed only the remaining tracked dirs — ownerless and never

# personal_dir — a catastrophic wipe (#1660). remove_directory now

# removes exactly this directory's chunks and leaves the rest intact.

if self.rag_manager:

try:

self.rag_manager.remove_directory(directory)

except Exception as e:

logger.error(f"Failed to remove directory from RAG index: {e}")

else:

logger.info(f"Directory not in index: {directory}")

def rename_directory(self, old_directory: str, new_directory: str, *, path_map: Dict[str, str] = None):

"""Rewrite tracked directory and excluded-file paths after an owner rename."""

old_directory = os.path.abspath(old_directory)

new_directory = os.path.abspath(new_directory)

path_map = {os.path.abspath(k): os.path.abspath(v) for k, v in (path_map or {}).items()}

def rewrite(path: str) -> str:

abs_path = os.path.abspath(path)

mapped = path_map.get(abs_path)

if mapped:

return mapped

if abs_path == old_directory:

return new_directory

if abs_path.startswith(old_directory + os.sep):

return new_directory + abs_path[len(old_directory):]

return abs_path

changed_dirs = False

rewritten_dirs = []

for directory in self.indexed_directories:

rewritten = rewrite(directory)

changed_dirs = changed_dirs or rewritten != os.path.abspath(directory)

if rewritten not in rewritten_dirs:

rewritten_dirs.append(rewritten)

if changed_dirs:

self.indexed_directories = rewritten_dirs

self.save_directories()

changed_excluded = False

rewritten_excluded = set()

for path in self.excluded_files:

rewritten = rewrite(path)

changed_excluded = changed_excluded or rewritten != os.path.abspath(path)

rewritten_excluded.add(rewritten)

if changed_excluded:

self.excluded_files = rewritten_excluded

self._save_excluded()

if changed_dirs or changed_excluded:

self.refresh_index()

def get_indexed_directories(self):

"""Get the list of all indexed directories."""

return self.indexed_directories.copy()

def refresh_index(self):

"""Refresh the document index including all tracked directories."""

self.index = []

# Index the base personal directory

base_files = load_personal_index(self.personal_dir)

for f in base_files:

if os.path.abspath(f.get("path", "")) in self.excluded_files:

continue

f['source_dir'] = self.personal_dir

self.index.append(f)

# Index additional directories

for directory in self.indexed_directories:

if not os.path.exists(directory):

logger.warning(f"Directory no longer exists: {directory}")

continue

if not os.path.isdir(directory):

logger.warning(f"Path is not a directory: {directory}")

continue

# Load files from this directory

dir_files = load_personal_index(directory)

for f in dir_files:

if os.path.abspath(f.get("path", "")) in self.excluded_files:

continue

# Update the name to include the directory for clarity

f['source_dir'] = directory

f['name'] = f"{os.path.basename(directory)}/{f['name']}"

self.index.append(f)

logger.info(f"Refreshed index: {len(self.index)} documents from {len(self.indexed_directories) + 1} directories")

def retrieve(self, query: str, k: int = 5) -> List[str]:

"""Retrieve relevant documents for a query."""

return retrieve_personal(self.index, query, k, self.rag_manager)

def get_file_list(self) -> List[Dict[str, Any]]:

"""Get list of indexed files with metadata."""

return [{"name": f["name"], "size": f["size"]} for f in self.index]

def get_stats(self) -> Dict[str, Any]:

"""Get statistics about indexed documents."""

total_docs = len(self.index)

total_chunks = sum(len(doc.get('chunks', [])) for doc in self.index)

total_size = sum(doc.get('size', 0) for doc in self.index)

extensions = {}

for doc in self.index:

ext = os.path.splitext(doc['path'])[1]

extensions[ext] = extensions.get(ext, 0) + 1

return {

'total_documents': total_docs,

'total_chunks': total_chunks,

'total_size_bytes': total_size,

'total_size_mb': round(total_size / (1024 * 1024), 2),

'file_types': extensions,

'directories_count': len(self.indexed_directories) + 1,

'base_directory': self.personal_dir,

'additional_directories': self.indexed_directories

}

def index_all_directories(self):

"""Re-index all tracked directories in the RAG system."""

if not self.rag_manager:

logger.warning("No RAG manager available for indexing")

return

success_count = 0

failure_count = 0

# Index the base personal directory

try:

result = self.rag_manager.index_personal_documents(self.personal_dir)

if result.get('success'):

success_count += 1

logger.info(f"Indexed base directory: {self.personal_dir}")

except Exception as e:

failure_count += 1

logger.error(f"Failed to index base directory {self.personal_dir}: {e}")

# Index additional directories

for directory in self.indexed_directories:

if not os.path.exists(directory):

logger.warning(f"Skipping non-existent directory: {directory}")

failure_count += 1

continue

try:

result = self.rag_manager.index_personal_documents(directory)

if result.get('success'):

success_count += 1

logger.info(f"Indexed directory: {directory}")

else:

failure_count += 1

logger.error(f"Failed to index directory {directory}: {result.get('message')}")

except Exception as e:

failure_count += 1

logger.error(f"Failed to index directory {directory}: {e}")

logger.info(f"Indexing complete: {success_count} succeeded, {failure_count} failed")

return {"success": success_count, "failed": failure_count}

odysseus/src/personal_docs.py at dev · odysseus-dev/odysseus · GitHub

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