Feature/detect file duplication (#42)

* add hash
* add file utils
* add detect_file_duplication s3 implementation

amazon_s3/s3_config.md

@@ -23,6 +23,7 @@ s3: # contact the provider for the following information
   reprocess_failed_files_reference: !!str 'string' # Full path to a file or URL to Saia GetDocuments API
   reprocess_valid_status_list: # List of Statuses to process, valid values Unknown, Starting, Failed, Pending, Success
   delete_local_folder: !!bool True|False (default) # Delete temporary folder if created
+  detect_file_duplication: !!bool True|False (default) # generate and compare a file hash on upload, discard duplications
   excluded_exts: # list of excluded extensions, by default it is suggested to include the following: raw, metadata
     - !!str 'metadata'
     - !!str 'raw'

amazon_s3/s3reader.py

@@ -11,8 +11,10 @@
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Union
 from urllib.parse import quote, unquote
+from saia_ingest.config import Defaults
 from saia_ingest.utils import detect_file_extension
 from saia_ingest.profile_utils import is_valid_profile, file_upload, file_delete, operation_log_upload, sync_failed_files, get_bearer_token, get_json_response_from_url
+from saia_ingest.file_utils import calculate_file_hash
 
 from llama_index import download_loader
 from llama_index.readers.base import BaseReader
@@ -57,6 +59,7 @@ def __init__(
         source_base_url: Optional[str] = None,
         source_doc_id: Optional[str] = None,
         alternative_document_service: Optional[Dict[str, str]] = None,
+        detect_file_duplication: Optional[bool] = False,
         **kwargs: Any,
     ) -> None:
         """Initialize S3 bucket and key, along with credentials if needed.
@@ -118,6 +121,7 @@ def __init__(
         self.alternative_document_service = alternative_document_service
         self.source_base_url = source_base_url
         self.source_doc_id = source_doc_id
+        self.detect_file_duplication = detect_file_duplication
 
         self.s3 = None
         self.s3_client = None
@@ -595,7 +599,7 @@ def rename_file(
             s3_file = key_prefix + file_name
             initial_metadata = self.get_metadata(s3_file)
             if self.use_augment_metadata:
-                user_metadata = self.augment_metadata(file_name, initial_metadata, timestamp_tag)
+                user_metadata = self.augment_metadata(folder_path, file_name, initial_metadata, timestamp_tag)
             extension_from_metadata = user_metadata.get(extension_tag, None)
             if user_metadata:
                 self.write_object_to_file(user_metadata, metadata_file_path)
@@ -627,6 +631,7 @@ def rename_file(
 
     def augment_metadata(
             self,
+            folder_path: str,
             document_name: str,
             input_metadata: dict,
             timestamp_tag: str = 'publishdate',
@@ -669,6 +674,11 @@ def augment_metadata(
                 initial_metadata[timestamp_tag] = formatted_date
                 initial_metadata['year'] = year
 
+            if self.detect_file_duplication:
+                file_path = f"{folder_path}/{document_name}"
+                file_hash = calculate_file_hash(file_path)
+                initial_metadata[Defaults.FILE_HASH] = file_hash
+
             if self.source_base_url is not None and self.source_doc_id is not None:
                 if doc_url is not None:
                     initial_metadata['url'] = doc_url

saia_ingest/config.py

@@ -57,3 +57,4 @@ class Defaults:
     PACKAGE_DESCRIPTION = "GeneXus Enterprise AI"
     PACKAGE_URL = "https://github.com/genexuslabs/saia-ingest/blob/main/README.md"
     PACKAGE_METADATA_POSTFIX = ".saia.metadata"
+    FILE_HASH = "hash"

saia_ingest/file_utils.py

@@ -0,0 +1,68 @@
+import json
+from pathlib import Path
+from typing import Dict, Any
+import hashlib
+import logging
+
+from saia_ingest.config import Defaults
+
+
+def calculate_file_hash(filepath: Path) -> str:
+    """Calculate the SHA-256 hash of a file."""
+    sha256 = hashlib.sha256()
+    try:
+        with open(filepath, 'rb') as f:
+            while chunk := f.read(4096):
+                sha256.update(chunk)
+    except FileNotFoundError:
+        logging.getLogger().error(f"File not found: {filepath}")
+        raise
+    except PermissionError:
+        logging.getLogger().error(f"Permission denied: {filepath}")
+        raise
+    return sha256.hexdigest()
+
+
+def are_files_identical(file1: Path, file2: Path) -> bool:
+    """Compare two files to see if they are identical by comparing their SHA-256 hashes."""
+    try:
+        return calculate_file_hash(file1) == calculate_file_hash(file2)
+    except Exception as e:
+        logging.getLogger().error(f"Error comparing files {file1} and {file2}: {e}")
+        return False
+
+
+def load_hashes_from_json(folder: Path) -> Dict[str, Any]:
+    """Load all existing hashes from JSON files in the folder."""
+    hash_index = {}
+    for json_file in folder.glob("*.json"):
+        try:
+            with json_file.open('r') as f:
+                data = json.load(f)
+                if Defaults.FILE_HASH in data:
+                    file_hash = data[Defaults.FILE_HASH]
+                    document_id = data["documentid"]
+                    if file_hash in hash_index:
+                        logging.getLogger().warning(f"{document_id} duplicate detected: using {hash_index[file_hash]}")
+                    else:
+                        hash_index[file_hash] = document_id
+        except (json.JSONDecodeError, FileNotFoundError) as e:
+            print(f"Error reading {json_file}: {e}")
+    return hash_index
+
+
+def check_for_duplicates(new_file: Path, folder: Path) -> bool:
+    """Check if the hash of a new file collides with existing hashes."""
+    # Load all existing hashes
+    hash_index = load_hashes_from_json(Path(folder))
+
+    # Calculate the hash of the new file
+    new_file_hash = calculate_file_hash(new_file)
+
+    if new_file_hash in hash_index:
+        print(f"Duplicate found! {new_file} matches {hash_index[new_file_hash]}")
+        return True
+    else:
+        print(f"No duplicates found for {new_file}.")
+        return False
+

saia_ingest/ingestor.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 import time
 from datetime import datetime, timezone
 import json
@@ -13,6 +14,7 @@
 from langchain.text_splitter import RecursiveCharacterTextSplitter
 
 from saia_ingest.config import Defaults
+from saia_ingest.file_utils import calculate_file_hash, load_hashes_from_json
 from saia_ingest.profile_utils import is_valid_profile, file_upload, file_delete, operation_log_upload, sync_failed_files, search_failed_to_delete
 from saia_ingest.rag_api import RagApi
 from saia_ingest.utils import get_yaml_config, get_metadata_file, load_json_file, search_failed_files, find_value_by_key
@@ -473,6 +475,7 @@ def ingest_s3(
         download_dir = s3_level.get('download_dir', None)
         verbose = s3_level.get('verbose', False)
         delete_downloaded_files = s3_level.get('delete_downloaded_files', False)
+        detect_file_duplication = s3_level.get('detect_file_duplication', False)
 
         # Saia
         saia_level = config.get('saia', {})
@@ -510,6 +513,7 @@ def ingest_s3(
             source_doc_id=source_doc_id,
             alternative_document_service=alternative_document_service,
             download_dir=download_dir,
+            detect_file_duplication=detect_file_duplication,
             verbose=verbose
             )
         loader.init_s3()
@@ -541,6 +545,17 @@ def ingest_s3(
                 file_paths = loader.get_files() if loader.alternative_document_service is None else loader.get_files_from_url()
 
                 saia_file_ids_to_delete = search_failed_to_delete(file_paths)
+                if detect_file_duplication and len(file_paths) > 0:
+                    hash_index = load_hashes_from_json(Path(download_dir))
+                    for new_file in file_paths:
+                        new_file_hash = calculate_file_hash(new_file)
+                        if new_file_hash in hash_index:
+                            document_id = hash_index[new_file_hash]
+                            file_name = os.path.basename(new_file)
+                            saia_file_ids_to_delete.append(hash_index[new_file_hash])
+                            file_paths.remove(new_file)
+                            logging.getLogger().warning(f"{file_name} duplicate discarded, using {document_id}")
+
                 with concurrent.futures.ThreadPoolExecutor(max_workers=max_parallel_executions) as executor:
                     futures = [executor.submit(ragApi.delete_profile_document, id, saia_profile) for id in saia_file_ids_to_delete]
                 concurrent.futures.wait(futures)

saia_ingest/profile_utils.py

@@ -5,6 +5,8 @@
 import requests
 import urllib3
 import json
+
+from saia_ingest.file_utils import calculate_file_hash
 from .log import AccumulatingLogHandler
 from .config import DefaultHeaders, Defaults
 
@@ -80,6 +82,8 @@ def file_upload(
             ret = False
         else:
             if save_answer:
+                file_crc = calculate_file_hash(file_path)
+                response_body[Defaults.FILE_HASH] = file_crc
                 with open(file_path + Defaults.PACKAGE_METADATA_POSTFIX, 'w') as file:
                     file.write(json.dumps(response_body, indent=2))
             end_time = time.time()