qubicon 1.0.0__tar.gz

qubicon-1.0.0/LICENSE

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qubicon-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: qubicon
+Version: 1.0.0
+Summary: Python library for the Qubicon Platform API
+Home-page: https://git.qub-lab.io/qub-client/qubicon-python-library
+Author: Stephan Karas
+Author-email: stephan.karas@qubicon-ag.com
+License: Apache License 2.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+License-File: LICENSE
+Requires-Dist: requests>=2.25.1
+Requires-Dist: rapidfuzz>=2.0.11
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: tabulate>=0.9.0
+Requires-Dist: rich>=13.5.1
+Requires-Dist: re>=2.2.1

qubicon-1.0.0/README.md

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+# Qubicon Python Library
+
+**Qubicon Python Library** is a Python interface that allows users to interact with Qubicon's bioprocess management platform programmatically. It offers tools for managing models, physical quantities, and processes, making it easier to automate complex tasks on the platform, streamline data acquisition, and integrate bioprocess data into various workflows.
+
+## Table of Contents
+
+1. [Installation](#installation)
+2. [Configuration](#configuration)
+3. [Authentication](#authentication)
+4. [Key Features](#key-features)
+   - [Models Management](#models-management)
+   - [Physical Quantities Management](#physical-quantities-management)
+   - [Processes and Data Extraction](#processes-and-data-extraction)
+5. [Functionality Overview](#functionality-overview)
+   - [Models](#models)
+   - [Processes](#processes)
+   - [Quantities](#quantities)
+6. [Usage Examples](#usage-examples)
+7. [License](#license)
+
+---
+
+## Installation
+
+To install the Qubicon Python Library, simply use pip:
+
+```bash
+pip install qubicon
+```
+
+---
+
+## Configuration
+
+After installation, configure the library by setting your base URL and any necessary credentials.
+
+### Example Configuration:
+
+```python
+from qubicon import Config
+
+config = Config(base_url='https://master.qub-lab.io/')
+```
+
+---
+
+## Authentication
+
+To authenticate with the Qubicon API, you need valid credentials (username and password). The `authenticate` method helps you securely log in to the API.
+
+### Example Authentication:
+
+```python
+from qubicon import authenticate
+
+# Authenticate with the API
+authenticate(config, username='your_username', password='your_password')
+```
+
+---
+
+## Key Features
+
+### 1. **Models Management**
+
+Manage computational models, import/export models, and retrieve details from the Qubicon API. The `Models` class provides several methods to interact with models stored in the Qubicon system.
+
+---
+
+## Functionality Overview
+
+### Models
+
+The `Models` class allows you to manage models by listing, retrieving, exporting, and importing them.
+
+#### `list()`
+Retrieves a list of all models available in the system.
+
+```python
+from qubicon.api.models import Models
+
+# Initialize the Models class
+models = Models(config)
+
+# List all models
+model_list = models.list()
+for model in model_list:
+    print(f"ID: {model['id']}, Name: {model['kpiName']}, Status: {model['status']}")
+```
+
+#### `get(model_id)`
+Retrieve the details of a specific model using its ID.
+
+```python
+# Fetch a specific model by its ID
+model_id = 123
+model_details = models.get(model_id)
+print(f"Model Name: {model_details['kpiName']}, Status: {model_details['status']}")
+```
+
+#### `get_model_dict()`
+Returns a dictionary mapping model names to their IDs.
+
+```python
+# Get a dictionary of model names and their IDs
+model_dict = models.get_model_dict()
+print(model_dict)
+```
+
+#### `import_model_from_json(file_path)`
+Imports a model from a JSON file.
+
+```python
+# Import a model from a JSON file
+models.import_model_from_json('path_to_model.json')
+```
+
+#### `export_model_to_json(model_id, output_file)`
+Exports a model to a JSON file.
+
+```python
+# Export a model to a JSON file
+models.export_model_to_json(423, 'exported_model.json')
+```
+
+---
+
+### Processes
+
+The `Processes` class provides methods to handle process data, including listing processes, retrieving channels, and extracting data.
+
+#### `list_processes()`
+Lists all available processes in the system.
+
+```python
+from qubicon.api.processes import Processes
+
+# Initialize the Processes class
+processes = Processes(config)
+
+# List all processes
+process_list = processes.list_processes()
+for process in process_list:
+    print(f"Process ID: {process['id']}, Name: {process['name']}")
+```
+
+#### `list_process_channels(process_id)`
+Lists all channels associated with a specific process.
+
+```python
+# List channels for a specific process
+process_id = 123
+channels = processes.list_process_channels(process_id)
+for channel in channels:
+    print(f"Channel ID: {channel['id']}, Name: {channel['name']}")
+```
+
+#### `extract_process_data(process_id, selected_channels, start_date, end_date, granularity, output_file, output_format)`
+Extracts process data for the selected channels and saves it to a file (JSON or CSV).
+
+```python
+# Extract process data and save it as a CSV file
+selected_channels = [{'id': 1}, {'id': 2}]
+start_date = '1728622700000'
+end_date = '1728624500000'
+
+processes.extract_process_data(
+    process_id=123,
+    selected_channels=selected_channels,
+    start_date=start_date,
+    end_date=end_date,
+    granularity=60,
+    output_file='process_data.csv',
+    output_format='csv'
+)
+```
+
+#### `get_process_details(process_id)`
+Retrieves the start and end dates of a process by its ID.
+
+```python
+# Get process details
+start_date, end_date = processes.get_process_details(123)
+print(f"Process Start: {start_date}, Process End: {end_date}")
+```
+
+---
+
+### Quantities
+
+The `Quantities` class allows you to manage physical quantities and units on the Qubicon platform.
+
+#### `list()`
+Retrieves a list of all physical quantities available in the system.
+
+```python
+from qubicon.api.quantities import Quantities
+
+# Initialize the Quantities class
+quantities = Quantities(config)
+
+# List all physical quantities
+quantity_list = quantities.list()
+for quantity in quantity_list:
+    print(f"Quantity ID: {quantity['id']}, Name: {quantity['name']}")
+```
+
+#### `get(quantity_id)`
+Retrieves the details of a specific physical quantity by its ID.
+
+```python
+# Get details of a specific quantity
+quantity_id = 71
+quantity_details = quantities.get(quantity_id)
+print(f"Quantity Name: {quantity_details['name']}, Unit: {quantity_details['units'][0]['unit']}")
+```
+
+#### `create_physical_quantity(pq_name, unit_name)`
+Creates a new physical quantity with a specific unit.
+
+```python
+# Create a new physical quantity
+new_quantity = quantities.create_physical_quantity('New Flow Rate', 'mL/min')
+print(f"Created Quantity ID: {new_quantity['id']}")
+```
+
+#### `add_unit_to_existing_physical_quantity(pq_id, pq_name, unit_name)`
+Adds a new unit to an existing physical quantity.
+
+```python
+# Add a new unit to an existing physical quantity
+quantities.add_unit_to_existing_physical_quantity(71, 'Flow Rate', 'L/min')
+```
+
+#### `check_existing_physical_quantity(pq_name)`
+Checks if a physical quantity already exists by performing a fuzzy match on the name.
+
+```python
+# Check if a physical quantity exists
+existing_pq = quantities.check_existing_physical_quantity('Flow Rate')
+if existing_pq:
+    print(f"Found existing physical quantity: {existing_pq['name']}")
+```
+
+#### `check_existing_unit(physical_quantity, unit_name)`
+Checks if a specific unit exists within a physical quantity.
+
+```python
+# Check if a unit exists for a physical quantity
+existing_unit = quantities.check_existing_unit(existing_pq, 'L/min')
+if existing_unit:
+    print(f"Found existing unit: {existing_unit['unit']}")
+```
+
+#### `handle_physical_quantities(model_data)`
+Handles the creation and updating of physical quantities and units for both inputs and outputs of a model.
+
+```python
+# Automatically handle physical quantities for a model
+updated_model_data = quantities.handle_physical_quantities(model_data)
+print("Updated model with physical quantities:", updated_model_data)
+```
+
+---
+
+## Usage Examples
+
+### Full Example: Exporting and Importing Models
+
+```python
+from qubicon import Config, authenticate
+from qubicon.api.models import Models
+
+# Configuration and authentication
+config = Config(base_url='https://master.qub-lab.io/')
+authenticate(config, username='yourusername', password='yourpassword')
+
+# Initialize the Models class
+models = Models(config)
+
+# Export a model to JSON
+models.export_model_to_json(423, 'exported_model.json')
+
+# Import the model back into the system
+models.import_model_from_json('exported_model.json')
+```
+
+### Full Example: Extracting Process Data
+
+```python
+from qubicon import Config, authenticate
+from qubicon.api.processes import Processes
+
+# Configuration and authentication
+config = Config(base_url='https://master.qub-lab.io/')
+authenticate(config, username='yourusername', password='yourpassword')
+
+# Initialize the Processes class
+processes = Processes(config)
+
+# Define the process ID and selected channels
+process_id = 123
+selected_channels = [{'id': 1}, {'id': 2}]
+start_date = '1728622700000'
+end_date = '1728624500000'
+
+# Extract and save data
+processes.extract_process_data(
+    process_id=process_id,
+    selected_channels=selected_channels,
+    start_date=start_date,
+    end_date=end_date,
+    granularity=148,
+    output_file=processed_data.csv'
+
+process_data.csv',
+    output_format='csv'
+)
+```
+
+---
+
+## License
+
+## License
+
+This project is licensed under the Apache License, Version 2.0. You may not use this project except in compliance with the License.
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0)
+
+You can view the full text of the license at the following link:
+
+[Apache 2.0 License](https://www.apache.org/licenses/LICENSE-2.0)
+
+```

qubicon-1.0.0/qubicon/__init__.py

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+from .config import Config
+from .auth import authenticate
+from .api.models import Models
+from .api.quantities import Quantities
+from .api.processes import Processes
+
+__all__ = [
+    'Config',
+    'authenticate',
+    'Models',
+    'Quantities',
+    'Processes',
+]

qubicon-1.0.0/qubicon/api/__init__.py

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+from .models import Models
+from .quantities import Quantities
+from .processes import Processes
+
+__all__ = [
+    'Models',
+    'Quantities',
+    'Processes',
+]