leaf-framework 0.1.0__tar.gz

leaf_framework-0.1.0/LICENSE

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leaf_framework-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: leaf-framework
+Version: 0.1.0
+Summary: LabEquipment Adapter Framework (LEAF)
+License: Apache-2.0
+Author: Matthew Crowther
+Author-email: b5044420@newcastle.ac.uk
+Requires-Python: >=3.12,<4.0
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: aioredis (>=1.3.1,<1.4.0)
+Requires-Dist: dateparser (>=1.2.0,<1.3.0)
+Requires-Dist: influxobject (>=0.0.1,<0.1.0)
+Requires-Dist: leaf-register (>=0.1.1,<0.2.0)
+Requires-Dist: nicegui (>=2.12.1,<2.13.0)
+Requires-Dist: paho-mqtt (>=2.1.0,<2.2.0)
+Requires-Dist: pyyaml (>=6.0.2,<6.1.0)
+Requires-Dist: redis (>=5.0.0b2,<5.1.0)
+Requires-Dist: requests (>=2.32.3,<2.33.0)
+Requires-Dist: watchdog (>=2.1.6,<2.2.0)
+Project-URL: Documentation, https://gitlab.com/LabEquipmentAdapterFramework/leaf/issues
+Project-URL: Homepage, https://gitlab.com/LabEquipmentAdapterFramework/leaf
+Project-URL: Repository, https://gitlab.com/LabEquipmentAdapterFramework/leaf
+Description-Content-Type: text/markdown
+
+# Adapter Framework for Equipment Monitoring and Control
+
+The Lab Equipment Adapter Framework (LEAF) implements an **Adapter Architecture**  designed to monitor and control various equipment types (e.g., bioreactors). The core principle of LEAF is to reduce the barrier to entry as much as possible to develop and deploy adapters for new equipment. The **EquipmentAdapters** are the functional equipment monitors composed of the rest of the **modules** (ProcessModules, PhaseModules, etc.) that perform specific tasks such as event monitoring, data processing, and output transmission.
+
+The complete documentation can be found [here](http://leaf.systemsbiology.nl). Also, the template to assist with developing adapters can be found [here](https://gitlab.com/LabEquipmentAdapterFramework/leaf-adapters/leaf-template).

leaf_framework-0.1.0/README.md

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+# Adapter Framework for Equipment Monitoring and Control
+
+The Lab Equipment Adapter Framework (LEAF) implements an **Adapter Architecture**  designed to monitor and control various equipment types (e.g., bioreactors). The core principle of LEAF is to reduce the barrier to entry as much as possible to develop and deploy adapters for new equipment. The **EquipmentAdapters** are the functional equipment monitors composed of the rest of the **modules** (ProcessModules, PhaseModules, etc.) that perform specific tasks such as event monitoring, data processing, and output transmission.
+
+The complete documentation can be found [here](http://leaf.systemsbiology.nl). Also, the template to assist with developing adapters can be found [here](https://gitlab.com/LabEquipmentAdapterFramework/leaf-adapters/leaf-template).

leaf_framework-0.1.0/leaf/adapters/core_adapters/continuous_experiment_adapter.py

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+from typing import Optional, Any
+
+from leaf.modules.process_modules.continous_module import ContinousProcess
+from leaf.modules.process_modules.process_module import ProcessModule
+from leaf.modules.phase_modules.start import StartPhase
+from leaf.modules.phase_modules.stop import StopPhase
+from leaf.modules.phase_modules.measure import MeasurePhase
+from leaf.modules.phase_modules.initialisation import InitialisationPhase
+
+from leaf_register.metadata import MetadataManager
+from leaf.error_handler.error_holder import ErrorHolder
+
+from leaf.modules.input_modules.event_watcher import EventWatcher
+from leaf.modules.input_modules.external_event_watcher import ExternalEventWatcher
+from leaf.modules.output_modules.output_module import OutputModule
+
+from leaf.adapters.equipment_adapter import EquipmentAdapter
+from leaf.adapters.equipment_adapter import AbstractInterpreter
+
+
+class ContinuousExperimentAdapter(EquipmentAdapter):
+    """
+    Adapter that implements a continuous process workflow for equipment 
+    without defined experiment start/stop boundaries.
+    
+    It runs the measurement process continuously and wraps start/stop/details
+    in a parallel control process.
+    """
+
+    def __init__(
+        self,
+        instance_data: dict[str, Any],
+        watcher: EventWatcher,
+        output: OutputModule,
+        interpreter: AbstractInterpreter,
+        maximum_message_size: Optional[int] = 1,
+        error_holder: Optional[ErrorHolder] = None,
+        metadata_manager: Optional[MetadataManager] = None,
+        experiment_timeout: Optional[int] = None,
+        external_watcher: Optional[ExternalEventWatcher] = None,
+    ):
+        """
+        Initialise the ContinuousExperimentAdapter.
+
+        Args:
+            instance_data (dict): Configuration and metadata for this adapter.
+            watcher (EventWatcher): Input module that monitors raw data/events.
+            output (OutputModule): Output module to transmit processed data.
+            interpreter (AbstractInterpreter): Parses and transforms raw inputs.
+            maximum_message_size (Optional[int]): Limit for batching measurement messages.
+            error_holder (Optional[ErrorHolder]): Shared error collector.
+            metadata_manager (Optional[MetadataManager]): Metadata manager instance.
+            experiment_timeout (Optional[int]): Optional timeout between measurements.
+            external_watcher (Optional[ExternalEventWatcher]): Optional external input module.
+        """
+        # Initialize phases
+        start_p = StartPhase(metadata_manager)
+        stop_p = StopPhase(metadata_manager)
+        measure_p = MeasurePhase(metadata_manager, maximum_message_size=maximum_message_size)
+        details_p = InitialisationPhase(metadata_manager)
+
+        # Set up continuous and control processes
+        measurement_process = ContinousProcess(
+            output,
+            measure_p,
+            metadata_manager=metadata_manager,
+            error_holder=error_holder
+        )
+
+        self._control_process = ProcessModule(
+            output,
+            [start_p, stop_p, details_p],
+            metadata_manager=metadata_manager,
+            error_holder=error_holder
+        )
+
+        processes = [measurement_process, self._control_process]
+
+        super().__init__(
+            instance_data,
+            watcher,
+            output,
+            processes,
+            interpreter,
+            metadata_manager=metadata_manager,
+            error_holder=error_holder,
+            experiment_timeout=experiment_timeout,
+            external_watcher=external_watcher
+        )
+
+    def start(self) -> None:
+        """
+        Trigger the start phase and launch the adapter loop.
+
+        Injects a synthetic start message via the control process
+        to initialise any start-specific logic or output.
+        """
+        start_topic = self._metadata_manager.experiment.start
+        self._control_process.process_input(start_topic, {})
+        super().start()

leaf_framework-0.1.0/leaf/adapters/core_adapters/discrete_experiment_adapter.py

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+from typing import Optional, Any
+
+from leaf.modules.process_modules.discrete_module import DiscreteProcess
+from leaf.modules.phase_modules.start import StartPhase
+from leaf.modules.phase_modules.stop import StopPhase
+from leaf.modules.phase_modules.measure import MeasurePhase
+from leaf.modules.phase_modules.initialisation import InitialisationPhase
+
+from leaf_register.metadata import MetadataManager
+from leaf.error_handler.error_holder import ErrorHolder
+
+from leaf.modules.input_modules.event_watcher import EventWatcher
+from leaf.modules.input_modules.external_event_watcher import ExternalEventWatcher
+from leaf.modules.output_modules.output_module import OutputModule
+
+from leaf.adapters.equipment_adapter import EquipmentAdapter, AbstractInterpreter
+
+
+class DiscreteExperimentAdapter(EquipmentAdapter):
+    """
+    Adapter that implements a discrete start-stop process workflow.
+
+    It sets up individual phases for start, stop, measure, and details.
+    The process is triggered by incoming events, not continuous monitoring.
+    """
+
+    def __init__(
+        self,
+        instance_data: dict[str, Any],
+        watcher: EventWatcher,
+        output: OutputModule,
+        interpreter: AbstractInterpreter,
+        maximum_message_size: Optional[int] = 1,
+        error_holder: Optional[ErrorHolder] = None,
+        metadata_manager: Optional[MetadataManager] = None,
+        experiment_timeout: Optional[int] = None,
+        external_watcher: Optional[ExternalEventWatcher] = None,
+    ):
+        """
+        Initialise the DiscreteExperimentAdapter.
+
+        Args:
+            instance_data (dict): Configuration and instance-level metadata.
+            watcher (EventWatcher): Monitors input events to trigger phase execution.
+            output (OutputModule): Module to transmit processed data externally.
+            interpreter (AbstractInterpreter): Translates raw data into structured output.
+            maximum_message_size (Optional[int]): Max batch size for messages in MeasurePhase.
+            error_holder (Optional[ErrorHolder]): Shared error container.
+            metadata_manager (Optional[MetadataManager]): Optional metadata manager.
+            experiment_timeout (Optional[int]): Max time allowed between measurements.
+            external_watcher (Optional[ExternalEventWatcher]): Input for out-of-band events (optional).
+        """
+        # Initialize phase modules
+        start_p = StartPhase(metadata_manager)
+        stop_p = StopPhase(metadata_manager)
+        measure_p = MeasurePhase(metadata_manager, 
+                                 maximum_message_size=maximum_message_size)
+        details_p = InitialisationPhase(metadata_manager)
+
+        # Combine into a discrete process
+        phases = [start_p, measure_p, stop_p, details_p]
+        processes = [DiscreteProcess(output, phases)]
+
+        super().__init__(
+            instance_data,
+            watcher,
+            output,
+            processes,
+            interpreter,
+            metadata_manager=metadata_manager,
+            error_holder=error_holder,
+            experiment_timeout=experiment_timeout,
+            external_watcher=external_watcher
+        )

leaf_framework-0.1.0/leaf/adapters/core_adapters/upload_adapter.py

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+from typing import Optional, Any
+
+from leaf.modules.process_modules.upload_module import UploadProcess
+from leaf.modules.phase_modules.start import StartPhase
+from leaf.modules.phase_modules.stop import StopPhase
+from leaf.modules.phase_modules.measure import MeasurePhase
+from leaf.modules.phase_modules.initialisation import InitialisationPhase
+
+from leaf.modules.input_modules.file_watcher import FileWatcher
+from leaf.modules.input_modules.external_event_watcher import ExternalEventWatcher
+from leaf.modules.output_modules.output_module import OutputModule
+
+from leaf_register.metadata import MetadataManager
+from leaf.error_handler.error_holder import ErrorHolder
+
+from leaf.adapters.equipment_adapter import EquipmentAdapter
+from leaf.adapters.equipment_adapter import AbstractInterpreter
+
+
+class UploadAdapter(EquipmentAdapter):
+    """
+    Adapter for equipment that stores data to a file all at once,
+    or where data must be manually uploaded into a watched directory.
+
+    This adapter uses a file watcher to detect new uploads and processes
+    the data through an artificial start-measure-stop sequence.
+    """
+
+    def __init__(
+        self,
+        instance_data: dict[str, Any],
+        output: OutputModule,
+        interpreter: AbstractInterpreter,
+        watch_dir: Optional[str] = None,
+        maximum_message_size: Optional[int] = 1,
+        error_holder: Optional[ErrorHolder] = None,
+        metadata_manager: Optional[MetadataManager] = None,
+        experiment_timeout: Optional[int] = None,
+        external_watcher: Optional[ExternalEventWatcher] = None,
+    ):
+        """
+        Initialise the UploadAdapter.
+
+        Args:
+            instance_data (dict): Instance-level configuration and metadata.
+            output (OutputModule): The output module used to transmit parsed data.
+            interpreter (AbstractInterpreter): Parses and translates raw data.
+            watch_dir (Optional[str]): Directory path to monitor for uploaded files.
+            maximum_message_size (Optional[int]): Max number of messages per transmission.
+            error_holder (Optional[ErrorHolder]): Error tracking object.
+            metadata_manager (Optional[MetadataManager]): Optional metadata manager.
+            experiment_timeout (Optional[int]): Timeout between measurements (not used here).
+            external_watcher (Optional[ExternalEventWatcher]): Optional listener for external inputs.
+        """
+        # Input module: watches a local directory
+        watcher = FileWatcher(watch_dir, metadata_manager, 
+                              error_holder=error_holder)
+
+        # Initialize discrete phases
+        start_p = StartPhase(metadata_manager)
+        stop_p = StopPhase(metadata_manager)
+        measure_p = MeasurePhase(metadata_manager, 
+                                 maximum_message_size=maximum_message_size)
+        details_p = InitialisationPhase(metadata_manager)
+
+        # Combine phases into a process
+        phases = [start_p, measure_p, stop_p, details_p]
+        processes = [UploadProcess(output, phases)]
+
+        super().__init__(
+            instance_data,
+            watcher,
+            output,
+            processes,
+            interpreter,
+            metadata_manager=metadata_manager,
+            error_holder=error_holder,
+            experiment_timeout=experiment_timeout,
+            external_watcher=external_watcher,
+        )