biothoth 0.1.0__tar.gz

biothoth-0.1.0/LICENSE

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
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+other than an Application or a Combined Work as defined below.
+
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+permanent authorization for you to choose that version for the
+Library.

biothoth-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: biothoth
+Version: 0.1.0
+Summary: The CLI for Biothoth.
+Author-email: Biothoth <hello@biothoth.com>
+License: LGPL-3.0-or-later
+Project-URL: Homepage, https://www.biothoth.com
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: keyring
+Requires-Dist: requests
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# Biothoth CLI
+
+A powerful command-line interface for interacting with Biothoth AI services.
+
+## Installation
+
+```bash
+pip install biothoth
+```
+
+##Getting Started
+
+Before using Biothoth CLI, you'll need to authenticate with your credentials:
+
+```bash
+biothoth auth
+```
+You'll be prompted to enter your email and secret token. These credentials will be securely stored for future use.
+
+## Uploading Files
+
+To upload a file to Biothoth, use the following command:
+
+```bash
+biothoth upload [path]
+```
+
+The "path" can point to a local file or directory.
+
+To upload to a specific directory, use the following command:
+
+```bash
+biothoth upload [path] --destination folder/
+```
+
+
+## Local Development
+
+To run the CLI locally, you can use the following command:
+
+```bash
+python uninstall biothoth
+pip install -e .
+```
+

biothoth-0.1.0/README.md

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+# Biothoth CLI
+
+A powerful command-line interface for interacting with Biothoth AI services.
+
+## Installation
+
+```bash
+pip install biothoth
+```
+
+##Getting Started
+
+Before using Biothoth CLI, you'll need to authenticate with your credentials:
+
+```bash
+biothoth auth
+```
+You'll be prompted to enter your email and secret token. These credentials will be securely stored for future use.
+
+## Uploading Files
+
+To upload a file to Biothoth, use the following command:
+
+```bash
+biothoth upload [path]
+```
+
+The "path" can point to a local file or directory.
+
+To upload to a specific directory, use the following command:
+
+```bash
+biothoth upload [path] --destination folder/
+```
+
+
+## Local Development
+
+To run the CLI locally, you can use the following command:
+
+```bash
+python uninstall biothoth
+pip install -e .
+```
+

biothoth-0.1.0/biothoth/main.py

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+import warnings
+warnings.filterwarnings("ignore")
+
+import os
+import json
+from pathlib import Path
+import click
+import keyring
+import requests
+from typing import List
+import mimetypes
+from tqdm import tqdm
+import math
+
+CONFIG_DIR = Path.home() / '.biothoth'
+CONFIG_FILE = CONFIG_DIR / 'config.json'
+SERVICE_NAME = 'biothoth'
+
+URL_BASE = "https://www.biothoth.com/api"
+# URL_BASE = "http://localhost:3000/api"
+
+# File size constants
+MULTIPART_THRESHOLD = 3 * 1024 * 1024 * 1024  # 3GB
+CHUNK_SIZE = 50 * 1024 * 1024  # 50MB
+
+def load_credentials():
+    """Load credentials from config file if they exist"""
+    if CONFIG_FILE.exists():
+        with open(CONFIG_FILE, 'r') as f:
+            return json.load(f)
+    return None
+
+def save_credentials(email, token):
+    """Save credentials to config file"""
+    CONFIG_DIR.mkdir(exist_ok=True)
+    credentials = {
+        'email': email,
+        'token': token
+    }
+    with open(CONFIG_FILE, 'w') as f:
+        json.dump(credentials, f)
+
+def get_credentials():
+    """Get credentials from system keyring"""
+    email = keyring.get_password(SERVICE_NAME, 'email')
+    token = keyring.get_password(SERVICE_NAME, 'token')
+    return email, token
+
+def save_credentials_system(email, token):
+    """Save credentials to system keyring"""
+    keyring.set_password(SERVICE_NAME, 'email', email)
+    keyring.set_password(SERVICE_NAME, 'token', token)
+
+@click.group()
+def cli():
+    """Biothoth CLI tool"""
+    pass
+
+@cli.command()
+def auth():
+    """Authenticate with Biothoth"""
+    # Check if credentials already exist
+    existing_email, existing_token = get_credentials()
+    if existing_email and existing_token:
+        if not click.confirm('Credentials already exist. Do you want to overwrite them?'):
+            click.echo('Authentication cancelled.')
+            return
+
+    email = click.prompt('Please enter your email')
+    token = click.prompt('Please enter your secret token', hide_input=True)
+    
+    # Verify credentials before saving
+    click.echo('Verifying credentials...')
+    try:
+        # Test credentials by requesting a presigned URL for a test file
+        bucket_name = "magicode-user-data-store"
+        verify_response = requests.post(
+            f'{URL_BASE}/s3-cli',
+            params={'bucket': bucket_name},
+            json={
+                'email': email,
+                'secretKey': token,
+                'fileName': 'test-verification.txt',
+            }
+        )
+        
+        if verify_response.status_code != 200:
+            click.echo(f'Invalid credentials. Authentication failed.', err=True)
+            return
+            
+        click.echo('Credentials verified successfully.')
+        save_credentials(email, token)
+        save_credentials_system(email, token)
+        click.echo('Credentials saved.')
+    except Exception as e:
+        click.echo(f'Error verifying credentials: {str(e)}', err=True)
+
+@cli.command()
+def logout():
+    """Clear stored credentials"""
+    try:
+        keyring.delete_password(SERVICE_NAME, 'email')
+        keyring.delete_password(SERVICE_NAME, 'token')
+        click.echo('Logged out successfully.')
+    except keyring.errors.PasswordDeleteError:
+        click.echo('No credentials found.')
+
+@cli.command()
+@click.argument('source')
+@click.option('--destination', default='', help='Destination path to prepend to uploaded files (should end with /)')
+def upload(source: str, destination: str):
+    """Upload a file or folder to Biothoth
+    
+    SOURCE: Path to the file or folder to upload
+    """
+    # Get credentials
+    email, token = get_credentials()
+    if not email or not token:
+        click.echo('Please authenticate first using the auth command.', err=True)
+        return
+
+    # Validate destination format if provided
+    if destination and not destination.endswith('/'):
+        click.echo('Destination path must end with a forward slash (/)', err=True)
+        return
+
+    path = Path(source)
+    if not path.exists():
+        click.echo(f'Path does not exist: {path}', err=True)
+        return
+
+    files_to_upload: List[Path] = []
+    folders_to_upload: List[Path] = []
+    
+    # Collect all files and folders
+    if path.is_file():
+        files_to_upload.append(path)
+    else:
+        # Collect all subdirectories and files (skip root folder itself)
+        for item in path.rglob('*'):
+            if item.is_file():
+                files_to_upload.append(item)
+            elif item.is_dir():
+                folders_to_upload.append(item)
+
+    total_items = len(files_to_upload) + len(folders_to_upload)
+    error = False 
+    errored_items = []
+    current_index = 0
+
+    # Upload empty content for folders first
+    for folder_path in folders_to_upload:
+        current_index += 1
+        try:
+            click.echo(f'Creating folder {current_index}/{total_items}: {folder_path}/')
+            
+            # Get relative path for the folder and prepend destination if provided
+            relative_path = folder_path.relative_to(path.parent)
+            folder_key = str(relative_path) + '/' if not str(relative_path).endswith('/') else str(relative_path)
+            if destination:
+                folder_key = destination + folder_key
+
+            # bucket name depends on the destination 
+            bucket_name = "magicode-user-data-store"
+            
+            # Get presigned URL
+            presigned_response = requests.post(
+                f'{URL_BASE}/s3-cli',
+                params={'bucket': bucket_name},
+                json={
+                    'email': email,
+                    'secretKey': token,
+                    'fileName': folder_key,
+                }
+            )
+
+            if presigned_response.status_code != 200:
+                error = True
+                errored_items.append(folder_path)
+                continue
+
+            presigned_data = presigned_response.json()
+            presigned_url = presigned_data['presignedUrl']
+
+            # Upload empty content for folder
+            upload_response = requests.put(
+                presigned_url,
+                data=b'',
+                headers={
+                    'Content-Type': 'application/x-directory',
+                    'Content-Length': '0'
+                }
+            )
+
+            if upload_response.status_code not in (200, 204):
+                error = True
+                errored_items.append(folder_path)
+                continue
+
+        except Exception as e:
+            error = True
+            errored_items.append(folder_path)
+            continue
+
+    # Upload files
+    for file_path in files_to_upload:
+        current_index += 1
+        try:
+            click.echo(f'Uploading file {current_index}/{total_items}: {file_path}')
+            
+            # Get relative path for the file and prepend destination if provided
+            relative_path = file_path.relative_to(path.parent)
+            file_key = str(relative_path)
+            if destination:
+                file_key = destination + file_key
+
+            # bucket name depends on the destination 
+            bucket_name = "magicode-user-data-store"
+            
+            # Get file size
+            file_size = os.path.getsize(file_path)
+            content_type = mimetypes.guess_type(file_path)[0] or 'application/octet-stream'
+            
+            # Check if file is large enough for multipart upload
+            if file_size > MULTIPART_THRESHOLD:
+                # Use multipart upload for large files
+                if not upload_large_file(file_path, file_key, bucket_name, email, token, content_type, file_size):
+                    error = True
+                    errored_items.append(file_path)
+            else:
+                # Use regular upload for smaller files
+                # Get presigned URL
+                presigned_response = requests.post(
+                    f'{URL_BASE}/s3-cli',
+                    params={'bucket': bucket_name},
+                    json={
+                        'email': email,
+                        'secretKey': token,
+                        'fileName': file_key,
+                    }
+                )
+
+                if presigned_response.status_code != 200:
+                    error = True
+                    errored_items.append(file_path)
+                    continue
+
+                presigned_data = presigned_response.json()
+                presigned_url = presigned_data['presignedUrl']
+
+                # Upload file using presigned URL with progress bar
+                with open(file_path, 'rb') as f:
+                    with tqdm(total=file_size, unit='B', unit_scale=True, unit_divisor=1024) as pbar:
+                        file_data = f.read()
+                        
+                        upload_response = requests.put(
+                            presigned_url,
+                            data=file_data,
+                            headers={
+                                'Content-Type': content_type,
+                                'Content-Length': str(file_size)
+                            }
+                        )
+                        pbar.update(file_size)  # Ensure bar reaches 100%
+
+                if upload_response.status_code not in (200, 204):
+                    error = True
+                    errored_items.append(file_path)
+                    continue
+
+        except Exception as e:
+            click.echo(f'Error uploading {file_path}: {str(e)}', err=True)
+            error = True
+            errored_items.append(file_path)
+            continue
+
+    if error:
+        click.echo(f'Upload has completed with errors.') 
+        click.echo(f'The following items were not uploaded:') 
+        for item in errored_items: 
+            click.echo(f'  - {item}') 
+        click.echo(f'Please check your credentials and try again.')
+    else: 
+        click.echo('Upload completed successfully.')
+
+def upload_large_file(file_path, file_key, bucket_name, email, token, content_type, file_size):
+    """Upload a large file using multipart upload"""
+    click.echo(f'File size is {file_size/1024/1024/1024:.2f} GB. Using multipart upload...')
+    
+    # Calculate number of parts
+    num_parts = math.ceil(file_size / CHUNK_SIZE)
+    
+    try:
+        # 1. Initiate multipart upload
+        initiate_response = requests.post(
+            f'{URL_BASE}/s3-cli-multipart',
+            params={'bucket': bucket_name, 'action': 'initiate'},
+            json={
+                'email': email,
+                'secretKey': token,
+                'fileName': file_key,
+                'contentType': content_type
+            }
+        )
+        
+        if initiate_response.status_code != 200:
+            click.echo(f'Failed to initiate multipart upload: {initiate_response.text}', err=True)
+            return False
+            
+        initiate_data = initiate_response.json()
+        upload_id = initiate_data['uploadId']
+        s3_key = initiate_data['key']
+        
+        click.echo(f'Initiated multipart upload with ID: {upload_id}')
+        
+        # 2. Upload parts
+        part_info = []
+        
+        with tqdm(total=num_parts, desc="Uploading parts", unit="part") as pbar:
+            for part_number in range(1, num_parts + 1):
+                # Get presigned URLs for this part
+                urls_response = requests.post(
+                    f'{URL_BASE}/s3-cli-multipart',
+                    params={'bucket': bucket_name, 'action': 'getUrls'},
+                    json={
+                        'email': email,
+                        'secretKey': token,
+                        'key': s3_key,
+                        'uploadId': upload_id,
+                        'partNumbers': [part_number]
+                    }
+                )
+                
+                if urls_response.status_code != 200:
+                    click.echo(f'Failed to get presigned URL for part {part_number}: {urls_response.text}', err=True)
+                    # Abort the multipart upload
+                    requests.post(
+                        f'{URL_BASE}/s3-cli-multipart',
+                        params={'bucket': bucket_name, 'action': 'abort'},
+                        json={
+                            'email': email,
+                            'secretKey': token,
+                            'key': s3_key,
+                            'uploadId': upload_id
+                        }
+                    )
+                    return False
+                
+                urls_data = urls_response.json()
+                part_url = urls_data['presignedUrls'][0]['presignedUrl']
+                
+                # Calculate byte range for this part
+                start_byte = (part_number - 1) * CHUNK_SIZE
+                end_byte = min(start_byte + CHUNK_SIZE, file_size)
+                part_size = end_byte - start_byte
+                
+                # Read the chunk from the file
+                with open(file_path, 'rb') as f:
+                    f.seek(start_byte)
+                    part_data = f.read(part_size)
+                
+                # Upload the part
+                part_response = requests.put(
+                    part_url,
+                    data=part_data,
+                    headers={'Content-Length': str(part_size)}
+                )
+                
+                if part_response.status_code not in (200, 204):
+                    click.echo(f'Failed to upload part {part_number}: {part_response.text}', err=True)
+                    # Abort the multipart upload
+                    requests.post(
+                        f'{URL_BASE}/s3-cli-multipart',
+                        params={'bucket': bucket_name, 'action': 'abort'},
+                        json={
+                            'email': email,
+                            'secretKey': token,
+                            'key': s3_key,
+                            'uploadId': upload_id
+                        }
+                    )
+                    return False
+                
+                # Get the ETag from the response headers
+                etag = part_response.headers.get('ETag')
+                part_info.append({
+                    'PartNumber': part_number,
+                    'ETag': etag
+                })
+                
+                pbar.update(1)
+        
+        # 3. Complete multipart upload
+        click.echo('Finalizing multipart upload...')
+        complete_response = requests.post(
+            f'{URL_BASE}/s3-cli-multipart',
+            params={'bucket': bucket_name, 'action': 'complete'},
+            json={
+                'email': email,
+                'secretKey': token,
+                'key': s3_key,
+                'uploadId': upload_id,
+                'parts': part_info
+            }
+        )
+        
+        if complete_response.status_code != 200:
+            click.echo(f'Failed to complete multipart upload: {complete_response.text}', err=True)
+            return False
+            
+        click.echo('Multipart upload completed successfully.')
+        return True
+        
+    except Exception as e:
+        click.echo(f'Error during multipart upload: {str(e)}', err=True)
+        # Try to abort the upload if possible
+        try:
+            if 'upload_id' in locals() and 's3_key' in locals():
+                requests.post(
+                    f'{URL_BASE}/s3-cli-multipart',
+                    params={'bucket': bucket_name, 'action': 'abort'},
+                    json={
+                        'email': email,
+                        'secretKey': token,
+                        'key': s3_key,
+                        'uploadId': upload_id
+                    }
+                )
+        except:
+            pass
+        return False
+
+if __name__ == '__main__':
+    cli()

biothoth-0.1.0/biothoth.egg-info/PKG-INFO

@@ -0,0 +1,64 @@
+Metadata-Version: 2.4
+Name: biothoth
+Version: 0.1.0
+Summary: The CLI for Biothoth.
+Author-email: Biothoth <hello@biothoth.com>
+License: LGPL-3.0-or-later
+Project-URL: Homepage, https://www.biothoth.com
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: keyring
+Requires-Dist: requests
+Requires-Dist: tqdm
+Dynamic: license-file
+
+# Biothoth CLI
+
+A powerful command-line interface for interacting with Biothoth AI services.
+
+## Installation
+
+```bash
+pip install biothoth
+```
+
+##Getting Started
+
+Before using Biothoth CLI, you'll need to authenticate with your credentials:
+
+```bash
+biothoth auth
+```
+You'll be prompted to enter your email and secret token. These credentials will be securely stored for future use.
+
+## Uploading Files
+
+To upload a file to Biothoth, use the following command:
+
+```bash
+biothoth upload [path]
+```
+
+The "path" can point to a local file or directory.
+
+To upload to a specific directory, use the following command:
+
+```bash
+biothoth upload [path] --destination folder/
+```
+
+
+## Local Development
+
+To run the CLI locally, you can use the following command:
+
+```bash
+python uninstall biothoth
+pip install -e .
+```
+

biothoth-0.1.0/biothoth.egg-info/SOURCES.txt

@@ -0,0 +1,11 @@
+LICENSE
+README.md
+pyproject.toml
+biothoth/__init__.py
+biothoth/main.py
+biothoth.egg-info/PKG-INFO
+biothoth.egg-info/SOURCES.txt
+biothoth.egg-info/dependency_links.txt
+biothoth.egg-info/entry_points.txt
+biothoth.egg-info/requires.txt
+biothoth.egg-info/top_level.txt

biothoth-0.1.0/biothoth.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

biothoth-0.1.0/biothoth.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+biothoth = biothoth.main:cli

biothoth-0.1.0/biothoth.egg-info/requires.txt

@@ -0,0 +1,4 @@
+click
+keyring
+requests
+tqdm

biothoth-0.1.0/biothoth.egg-info/top_level.txt

@@ -0,0 +1 @@
+biothoth

biothoth-0.1.0/pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "biothoth"
+version = "0.1.0"
+authors = [
+  { name="Biothoth", email="hello@biothoth.com" },
+]
+description = "The CLI for Biothoth."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+]
+license = {text = "LGPL-3.0-or-later"}
+dependencies = [
+    "click",
+    "keyring",
+    "requests",
+    "tqdm",
+]
+
+[project.urls]
+Homepage = "https://www.biothoth.com"
+
+[project.scripts]
+biothoth = "biothoth.main:cli" 

biothoth-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+