biosero-data-models 0.1.3__tar.gz

biosero_data_models-0.1.3/LICENSE

@@ -0,0 +1,202 @@
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biosero_data_models-0.1.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: biosero-data-models
+Version: 0.1.3
+Summary: A python library with client and contract code to work with the Data Services API
+Author-email: Pete Werner <peterwerner@biosero.com>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/biosero/data-models-python
+License-File: LICENSE
+Requires-Dist: anyio==4.4.0
+Requires-Dist: aiohttp==3.9.5
+Requires-Dist: certifi==2024.6.2
+Requires-Dist: charset-normalizer==3.3.2
+Requires-Dist: h11==0.14.0
+Requires-Dist: httpcore==1.0.5
+Requires-Dist: httpx==0.27.0
+Requires-Dist: idna==3.7
+Requires-Dist: jsonpickle==4.0.5
+Requires-Dist: requests==2.32.3
+Requires-Dist: sniffio==1.3.1
+Requires-Dist: rich==13.7.1
+Dynamic: license-file

biosero_data_models-0.1.3/README.md

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+# Data Models Python
+
+A Python library with client and contract code to interact with the Data Services API.
+
+## Requirements
+
+- Python 3.12.3
+
+## Build
+
+python setup.py sdist bdist_wheel
+
+
+## Installation
+```sh
+pip install biosero-0.1.0-py3-none-any.whl
+
+```
+
+### From PyPI (currently not available)
+
+```sh
+pip install biosero

biosero_data_models-0.1.3/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "biosero-data-models"
+version = "0.1.3"
+description = "A python library with client and contract code to work with the Data Services API"
+authors = [
+    { name="Pete Werner", email="peterwerner@biosero.com" }
+]
+license = {text = "Apache-2.0"}
+dependencies = [
+    "anyio==4.4.0",
+    "aiohttp==3.9.5",
+    "certifi==2024.6.2",
+    "charset-normalizer==3.3.2",
+    "h11==0.14.0",
+    "httpcore==1.0.5",
+    "httpx==0.27.0",
+    "idna==3.7",
+    "jsonpickle==4.0.5",
+    "requests==2.32.3",
+    "sniffio==1.3.1",
+    "rich==13.7.1"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/biosero/data-models-python"
+
+[project.scripts]
+# Example: script_name = "module:function"

biosero_data_models-0.1.3/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

biosero_data_models-0.1.3/src/biosero/datamodels/__init__.py

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+from .events import EventMessage, EventContext,LiquidTransferEvent, LocationChangedEvent, ModuleStatus, ModuleStatusUpdateEvent
+from .extensions import ExceptionExtensions, ObjectExtension, StringExtensions
+from .helpers import EnumHelper,HttpClientHelper, StringHelper, UniqueIdentifierProvider, well_helper
+from .measurement import Concentration, Evaluator, InventoryThreshold, inventorylevel, Location, MaterialState, Temperature, Volume, Weight, Coordinates
+from .ordering import Order, OrderPriority, OrderStatus, SchedulingStrategy, ModuleRestrictionStrategy
+from .parameters import Parameter, ParameterCollection, ParameterValueType
+from .resources import Identity, Plate, PlateType, CommonTypeIdentifiers
+from .restclients import EventClient, OrderClient, OrderScheduler
+from .adapter import OrderProcessor, TemplateRegistrar, ClientLibraryGenerator
+
+
+
+__all__ = ['EventMessage', 'OrderClient','EventContext', 'LiquidTransferEvent', 'LocationChangedEvent', 'ExceptionExtensions', 'ObjectExtension', 'StringExtensions', 'EnumHelper', 'HttpClientHelper', 'StringHelper', 'UniqueIdentifierProvider', 'well_helper', 'Concentration', 'Evaluator', 'InventoryThreshold', 'inventorylevel', 'Location', 'Coordinates', 'MaterialState', 'Temperature', 'Volume', 'Weight', 'Order', 'OrderPriority', 'OrderStatus', 'SchedulingStrategy', 'ModuleRestrictionStrategy', 'Parameter', 'ParameterCollection', 'ParameterValueType', 'Identity', 'Plate', 'PlateType', 'CommonTypeIdentifiers', 'EventClient', 'OrderProcessor', 'TemplateRegistrar', 'ClientLibraryGenerator', 'ModuleStatus', 'ModuleStatusUpdateEvent', 'OrderScheduler']

biosero_data_models-0.1.3/src/biosero/datamodels/adapter/__init__.py

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+from .decorators import parameter, action
+from .template_icons import Icons
+from .helpers import Helpers
+from .template_categories import Categories
+from .order_processer import OrderProcessor
+from .template_registrar import TemplateRegistrar
+from .generate_library import ClientLibraryGenerator
+
+__all__ = ['parameter', 'action', 'Icons', 'Helpers', 'Categories', 'OrderProcessor', 'TemplateRegistrar', 'ClientLibraryGenerator']

biosero_data_models-0.1.3/src/biosero/datamodels/adapter/decorators.py

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+import logging
+from biosero.datamodels.adapter.template_icons import Icons
+from rich.logging import RichHandler
+import functools
+
+logger = logging.getLogger("rich")
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(message)s",
+    handlers=[RichHandler(rich_tracebacks=True)]
+)
+
+def parameter(name=None, inputs=None, outputs=None, icon=Icons.CODE.value, category="Python", color="#FFFFFF"):
+    def decorator(func):
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            result = func(*args, **kwargs)
+            return result
+
+        # Attach the metadata to the wrapper function
+        wrapper._parameter_decorator = {
+            'name': name,
+            'inputs': inputs,
+            'outputs': outputs,
+            'icon': icon,
+            'category': category,
+            'color': color
+        }
+        
+        return wrapper
+    
+    return decorator
+
+def action(name=None):
+    def decorator(func):
+        @functools.wraps(func)  # Apply the wraps decorator here
+        def wrapper(*args, **kwargs):
+            logger.info(f"[blue]Action: {func.__name__} is being executed.[/blue]", extra={"markup": True})
+            result = func(*args, **kwargs)
+            return result
+        
+        # Attach the metadata to the wrapper function
+        wrapper._action_decorator = {
+            'name': name or func.__name__,
+            'inputs': [],
+            'outputs': []
+        }
+        
+        return wrapper
+    
+    return decorator

biosero_data_models-0.1.3/src/biosero/datamodels/adapter/generate_library.py

@@ -0,0 +1,154 @@
+import os
+import inspect
+import subprocess
+import sys
+import types
+from typing import Tuple, Any
+from biosero.datamodels.adapter.decorators import parameter
+from biosero.datamodels.adapter.helpers import Helpers
+
+
+class ClientLibraryGenerator:
+    CLASS_TEMPLATE = """
+from biosero.datamodels.adapter.decorators import parameter
+from biosero.datamodels.adapter.helpers import Helpers
+from typing import Tuple, Any
+
+class Actions(object):
+
+    def __init__(self, url):
+        self.helpers = Helpers(url)
+"""
+
+    METHOD_TEMPLATE = """
+    @parameter(name='{template_name}', inputs={inputs}, outputs={outputs})
+    def {name}(self, {params}) -> Tuple[{return_type}]:
+        return self.helpers.process_order()
+"""
+
+    def __init__(self, base_path: str, action_templates):
+        """
+        Initializes the client library generator.
+
+        :param base_path: The base directory where the client library will be generated.
+        :param action_templates: The imported action_templates module.
+        """
+        self.base_path = os.path.abspath(base_path)  # Ensure absolute path
+        self.package_dir = os.path.join(self.base_path, "src/dataservices/adapter")
+        self.dist_dir = os.path.join(self.base_path, "dist")
+        self.build_dir = os.path.join(self.base_path, "build")
+        self.egg_info_dir = os.path.join(self.base_path, "src/dataservices.egg-info")
+        self.action_templates = action_templates  # Pass action_templates dynamically
+
+    def extract_outputs(self, decorator):
+        """Extract the outputs from the parameter decorator."""
+        return decorator.get('outputs', [])
+
+    def generate_methods(self):
+        methods = []
+        for name in dir(self.action_templates):
+            method = getattr(self.action_templates, name)
+            if isinstance(method, types.FunctionType) and hasattr(method, '_parameter_decorator'):
+                methods.append(method)
+
+        generated_methods = []
+        for method in methods:
+            decorator = method._parameter_decorator
+            template_name = decorator['name']
+            print(f"Generating method for {template_name}")
+
+            name = method.__name__
+            sig = inspect.signature(method)
+            params = ", ".join(
+                [f"{p}: {t.annotation.__name__ if t.annotation != inspect._empty else 'Any'}"
+                 for p, t in sig.parameters.items()]
+            )
+            inputs = [p.replace("_", " ").title() for p in sig.parameters.keys()]
+            outputs = self.extract_outputs(decorator)
+
+            return_annotation = sig.return_annotation
+            if return_annotation is inspect._empty:
+                return_type = "Any"
+            elif hasattr(return_annotation, '__args__'):
+                return_type = ", ".join([t.__name__ for t in return_annotation.__args__])
+            else:
+                return_type = return_annotation.__name__
+
+            method_code = self.METHOD_TEMPLATE.format(
+                name=name,
+                template_name=template_name,
+                params=params,
+                inputs=inputs,
+                outputs=outputs,
+                return_type=return_type
+            )
+            generated_methods.append(method_code)
+        return generated_methods
+
+    def generate_client_library(self):
+        # Step 1: Create necessary directories
+        os.makedirs(self.package_dir, exist_ok=True)
+        os.makedirs(self.dist_dir, exist_ok=True)
+        os.makedirs(self.build_dir, exist_ok=True)
+
+        # Step 2: Create __init__.py files
+        self.create_init_file(os.path.join(self.base_path, "src/dataservices"))
+        self.create_init_file(self.package_dir)
+
+        # Step 3: Generate the Python file
+        with open(os.path.join(self.package_dir, "actions.py"), "w") as f:
+            class_code = self.CLASS_TEMPLATE + "\n".join(self.generate_methods())
+            f.write(class_code)
+
+        # Step 4: Create setup.py file
+        self.create_setup_file()
+
+        print(f"Client library generated successfully in {self.base_path}!")
+
+        # Step 5: Ensure wheel is installed
+        subprocess.run([sys.executable, "-m", "pip", "install", "wheel"], check=True)
+
+        # Step 6: Build the distribution files
+        self.build_distribution()
+
+    def create_init_file(self, path):
+        with open(os.path.join(path, "__init__.py"), "w") as init_file:
+            init_file.write("# This is the __init__.py file\n")
+
+    def create_setup_file(self):
+        setup_path = os.path.join(self.base_path, "setup.py")
+        with open(setup_path, "w") as setup_file:
+            setup_file.write(
+    f"""from setuptools import setup, find_packages
+
+setup(
+    name='dataservices',
+    version='0.1',
+    package_dir={{'': 'src'}},
+    packages=find_packages(where='src'),
+    install_requires=[
+        # Add your dependencies here
+    ],
+)
+"""
+)
+
+
+    def build_distribution(self):
+        try:
+            subprocess.run(
+                [sys.executable, os.path.join(self.base_path, "setup.py"), "sdist", "bdist_wheel"],
+                cwd=self.base_path,  # Ensure build output stays in base path
+                check=True
+            )
+            print(f"Distribution files generated successfully in {self.base_path}!")
+
+            # Ensure dataservices.egg-info is in the base path
+            if os.path.exists(self.egg_info_dir):
+                print(f"Egg info directory created: {self.egg_info_dir}")
+            else:
+                print("dataservices.egg-info not found. It may be created dynamically during install.")
+
+        except subprocess.CalledProcessError as e:
+            print(f"Error occurred while building distribution files: {e}")
+

biosero_data_models-0.1.3/src/biosero/datamodels/adapter/helpers.py

@@ -0,0 +1,109 @@
+import inspect
+from biosero.datamodels.adapter.decorators import parameter
+from biosero.datamodels.parameters import Parameter, ParameterValueType, ParameterCollection
+from biosero.datamodels.restclients import OrderClient
+from biosero.datamodels.ordering import Order, OrderStatus
+import time
+from typing import Tuple, get_type_hints
+
+class Helpers(object):
+
+    def __init__(self, data_services_url: str):
+
+        self.data_services_url = data_services_url
+    
+    def process_order(self):
+
+        type_mapping = {
+            str: ParameterValueType.STRING,
+            bool: ParameterValueType.BOOLEAN,
+            float: ParameterValueType.DOUBLE,
+            int: ParameterValueType.INTEGER,
+        }
+
+        # Get the current function's frame
+        frame = inspect.currentframe().f_back
+        # Get the current function's arguments
+        _, _, _, values = inspect.getargvalues(frame)
+        values = {k: v for k, v in values.items() if k != 'self'}
+        # Get the current function's name
+        func_name = frame.f_code.co_name
+        # Get the class object
+        cls = frame.f_locals['self'].__class__
+        # Get the function object from the class
+        func = getattr(cls, func_name)
+        # Access the decorator metadata
+        template_name = func._parameter_decorator['name']
+        inputs = func._parameter_decorator['inputs']
+        outputs = func._parameter_decorator['outputs']
+
+        type_hints = get_type_hints(func)
+
+        input_parameters = ParameterCollection()
+
+        for index, input_name in enumerate(inputs):
+            param = Parameter()
+            param.name = input_name
+            # Get the value based on the current index
+            param.value = list(values.values())[index]  # Assuming values is a dictionary
+            # Set the parameter value type based on type hints
+            param_type = type_hints.get(input_name.replace(" ", "_").lower(), str)
+            param.value_type = type_mapping.get(param_type, ParameterValueType.OTHER)
+            input_parameters.append(param)
+
+
+        # output_parameters = ParameterCollection()
+
+        # for index, output_name in enumerate(outputs):
+        #     param = Parameter()
+        #     param.name = output_name
+        #     # Get the value based on the current index
+        #     param.value = list(values.values())[index]  # Assuming values is a dictionary
+        #     # Set the parameter value type based on type hints
+        #     param_type = type_hints.get(output_name.replace(" ", "_").lower(), str)
+        #     param.value_type = type_mapping.get(param_type, ParameterValueType.OTHER)
+        #     output_parameters.append(param)
+        output_parameters = ParameterCollection()
+
+        for output_name in outputs:
+            param = Parameter()
+            param.name = output_name
+            param.value = None 
+            param_type = type_hints.get(output_name.replace(" ", "_").lower(), str)
+            param.value_type = type_mapping.get(param_type, ParameterValueType.OTHER)
+            output_parameters.append(param)
+
+        order = Order()
+
+        # Create the order
+        order_client = OrderClient(self.data_services_url)
+        order.moduleRestrictionStrategy = "NoRestriction"
+        order.templateName = template_name
+        order.createdBy = "data services action"
+        order.inputParameters = input_parameters.to_dict()
+        order.outputParameters = output_parameters.to_dict()
+
+        response = order_client.create_order(order)
+        return_order = order_client.get_order(response)
+
+        while return_order.status != OrderStatus.Complete.name:
+            print("Waiting for Order to Complete")
+            time.sleep(2)
+            return_order = order_client.get_order(response)
+
+            if return_order.status == OrderStatus.Error.name:
+                print("Order failed")
+                break
+
+        # Retrieve output parameters from the completed order
+        extracted_output_params = {param['name']: param['value'] for param in return_order.outputParameters}
+
+        tuple_output = ()
+
+        for output_name in outputs:
+
+            item = extracted_output_params.get(output_name)
+
+            tuple_output += (item,)
+
+        return tuple_output