Initial commit
This commit is contained in:
Zhongwei Li
334
skills/labarchive-integration/scripts/entry_operations.py
Executable file
334
skills/labarchive-integration/scripts/entry_operations.py
Executable file
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#!/usr/bin/env python3
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"""
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LabArchives Entry Operations
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Utilities for creating entries, uploading attachments, and managing notebook content.
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"""
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import argparse
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import sys
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import yaml
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import os
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from pathlib import Path
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from datetime import datetime
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def load_config(config_path='config.yaml'):
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"""Load configuration from YAML file"""
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try:
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with open(config_path, 'r') as f:
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return yaml.safe_load(f)
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except FileNotFoundError:
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print(f"❌ Configuration file not found: {config_path}")
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print(" Run setup_config.py first to create configuration")
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sys.exit(1)
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except Exception as e:
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print(f"❌ Error loading configuration: {e}")
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sys.exit(1)
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def init_client(config):
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"""Initialize LabArchives API client"""
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try:
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from labarchivespy.client import Client
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return Client(
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config['api_url'],
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config['access_key_id'],
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config['access_password']
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)
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except ImportError:
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print("❌ labarchives-py package not installed")
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print(" Install with: pip install git+https://github.com/mcmero/labarchives-py")
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sys.exit(1)
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def get_user_id(client, config):
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"""Get user ID via authentication"""
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import xml.etree.ElementTree as ET
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login_params = {
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'login_or_email': config['user_email'],
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'password': config['user_external_password']
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}
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try:
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response = client.make_call('users', 'user_access_info', params=login_params)
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if response.status_code == 200:
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uid = ET.fromstring(response.content)[0].text
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return uid
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else:
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print(f"❌ Authentication failed: HTTP {response.status_code}")
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print(f" Response: {response.content.decode('utf-8')[:200]}")
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sys.exit(1)
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except Exception as e:
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print(f"❌ Error during authentication: {e}")
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sys.exit(1)
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def create_entry(client, uid, nbid, title, content=None, date=None):
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"""Create a new entry in a notebook"""
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print(f"\n📝 Creating entry: {title}")
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# Prepare parameters
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params = {
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'uid': uid,
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'nbid': nbid,
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'title': title
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}
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if content:
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# Ensure content is HTML formatted
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if not content.startswith('<'):
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content = f'<p>{content}</p>'
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params['content'] = content
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if date:
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params['date'] = date
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try:
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response = client.make_call('entries', 'create_entry', params=params)
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if response.status_code == 200:
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print("✅ Entry created successfully")
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# Try to extract entry ID from response
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try:
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import xml.etree.ElementTree as ET
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root = ET.fromstring(response.content)
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entry_id = root.find('.//entry_id')
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if entry_id is not None:
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print(f" Entry ID: {entry_id.text}")
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return entry_id.text
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except:
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pass
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return True
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else:
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print(f"❌ Entry creation failed: HTTP {response.status_code}")
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print(f" Response: {response.content.decode('utf-8')[:200]}")
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return None
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except Exception as e:
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print(f"❌ Error creating entry: {e}")
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return None
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def create_comment(client, uid, nbid, entry_id, comment):
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"""Add a comment to an existing entry"""
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print(f"\n💬 Adding comment to entry {entry_id}")
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params = {
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'uid': uid,
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'nbid': nbid,
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'entry_id': entry_id,
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'comment': comment
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}
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try:
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response = client.make_call('entries', 'create_comment', params=params)
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if response.status_code == 200:
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print("✅ Comment added successfully")
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return True
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else:
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print(f"❌ Comment creation failed: HTTP {response.status_code}")
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return False
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except Exception as e:
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print(f"❌ Error creating comment: {e}")
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return False
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def upload_attachment(client, config, uid, nbid, entry_id, file_path):
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"""Upload a file attachment to an entry"""
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import requests
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file_path = Path(file_path)
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if not file_path.exists():
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print(f"❌ File not found: {file_path}")
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return False
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print(f"\n📎 Uploading attachment: {file_path.name}")
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print(f" Size: {file_path.stat().st_size / 1024:.2f} KB")
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url = f"{config['api_url']}/entries/upload_attachment"
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try:
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with open(file_path, 'rb') as f:
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files = {'file': f}
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data = {
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'uid': uid,
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'nbid': nbid,
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'entry_id': entry_id,
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'filename': file_path.name,
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'access_key_id': config['access_key_id'],
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'access_password': config['access_password']
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}
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response = requests.post(url, files=files, data=data)
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if response.status_code == 200:
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print("✅ Attachment uploaded successfully")
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return True
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else:
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print(f"❌ Upload failed: HTTP {response.status_code}")
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print(f" Response: {response.content.decode('utf-8')[:200]}")
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return False
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except Exception as e:
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print(f"❌ Error uploading attachment: {e}")
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return False
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def batch_upload(client, config, uid, nbid, entry_id, directory):
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"""Upload all files from a directory as attachments"""
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directory = Path(directory)
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if not directory.is_dir():
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print(f"❌ Directory not found: {directory}")
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return
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files = list(directory.glob('*'))
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files = [f for f in files if f.is_file()]
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if not files:
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print(f"❌ No files found in {directory}")
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return
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print(f"\n📦 Batch uploading {len(files)} files from {directory}")
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successful = 0
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failed = 0
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for file_path in files:
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if upload_attachment(client, config, uid, nbid, entry_id, file_path):
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successful += 1
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else:
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failed += 1
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print("\n" + "="*60)
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print(f"Batch upload complete: {successful} successful, {failed} failed")
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print("="*60)
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def create_entry_with_attachments(client, config, uid, nbid, title, content,
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attachments):
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"""Create entry and upload multiple attachments"""
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# Create entry
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entry_id = create_entry(client, uid, nbid, title, content)
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if not entry_id:
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print("❌ Cannot upload attachments without entry ID")
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return False
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# Upload attachments
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for attachment_path in attachments:
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upload_attachment(client, config, uid, nbid, entry_id, attachment_path)
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return True
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def main():
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"""Main command-line interface"""
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parser = argparse.ArgumentParser(
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description='LabArchives Entry Operations',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Create simple entry
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python3 entry_operations.py create --nbid 12345 --title "Experiment Results"
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# Create entry with content
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python3 entry_operations.py create --nbid 12345 --title "Results" \\
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--content "PCR amplification successful"
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# Create entry with HTML content
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python3 entry_operations.py create --nbid 12345 --title "Results" \\
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--content "<p>Results:</p><ul><li>Sample A: Positive</li></ul>"
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# Upload attachment to existing entry
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python3 entry_operations.py upload --nbid 12345 --entry-id 67890 \\
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--file data.csv
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# Batch upload multiple files
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python3 entry_operations.py batch-upload --nbid 12345 --entry-id 67890 \\
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--directory ./experiment_data/
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# Add comment to entry
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python3 entry_operations.py comment --nbid 12345 --entry-id 67890 \\
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--text "Follow-up analysis needed"
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"""
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)
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parser.add_argument('--config', default='config.yaml',
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help='Path to configuration file (default: config.yaml)')
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parser.add_argument('--nbid', required=True,
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help='Notebook ID')
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subparsers = parser.add_subparsers(dest='command', help='Command to execute')
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# Create entry command
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create_parser = subparsers.add_parser('create', help='Create new entry')
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create_parser.add_argument('--title', required=True, help='Entry title')
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create_parser.add_argument('--content', help='Entry content (HTML supported)')
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create_parser.add_argument('--date', help='Entry date (YYYY-MM-DD)')
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create_parser.add_argument('--attachments', nargs='+',
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help='Files to attach to the new entry')
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# Upload attachment command
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upload_parser = subparsers.add_parser('upload', help='Upload attachment to entry')
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upload_parser.add_argument('--entry-id', required=True, help='Entry ID')
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upload_parser.add_argument('--file', required=True, help='File to upload')
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# Batch upload command
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batch_parser = subparsers.add_parser('batch-upload',
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help='Upload all files from directory')
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batch_parser.add_argument('--entry-id', required=True, help='Entry ID')
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batch_parser.add_argument('--directory', required=True,
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help='Directory containing files to upload')
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# Comment command
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comment_parser = subparsers.add_parser('comment', help='Add comment to entry')
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comment_parser.add_argument('--entry-id', required=True, help='Entry ID')
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comment_parser.add_argument('--text', required=True, help='Comment text')
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args = parser.parse_args()
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if not args.command:
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parser.print_help()
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sys.exit(1)
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# Load configuration and initialize
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config = load_config(args.config)
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client = init_client(config)
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uid = get_user_id(client, config)
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# Execute command
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if args.command == 'create':
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if args.attachments:
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create_entry_with_attachments(
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client, config, uid, args.nbid, args.title,
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args.content, args.attachments
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)
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else:
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create_entry(client, uid, args.nbid, args.title,
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args.content, args.date)
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elif args.command == 'upload':
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upload_attachment(client, config, uid, args.nbid,
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args.entry_id, args.file)
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elif args.command == 'batch-upload':
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batch_upload(client, config, uid, args.nbid,
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args.entry_id, args.directory)
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elif args.command == 'comment':
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create_comment(client, uid, args.nbid, args.entry_id, args.text)
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if __name__ == '__main__':
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main()
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