synapse-sdk 1.0.0a70__tar.gz → 1.0.0a71__tar.gz

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synapse-sdk
-Version: 1.0.0a70
+Version: 1.0.0a71
 Summary: synapse sdk
 Author-email: datamaker <developer@datamaker.io>
 License: MIT

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk/loggers.py

@@ -110,7 +110,7 @@ class BaseLogger:
         if 'categories' not in self.metrics_record:
             self.metrics_record['categories'] = {}
 
-        self.metrics_record['categories'][category] = value
+        self.metrics_record['categories'].setdefault(category, {}).update(value)
 
     def log(self, action, data, file=None):
         raise NotImplementedError

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk/plugins/categories/export/actions/export.py

@@ -280,7 +280,18 @@ class ExportAction(Action):
             'proportion': 100,
         }
     }
-    metrics_categories = {'data_file', 'original_file'}
+    metrics_categories = {
+        'data_file': {
+            'stand_by': 0,
+            'failed': 0,
+            'success': 0,
+        },
+        'original_file': {
+            'stand_by': 0,
+            'failed': 0,
+            'success': 0,
+        },
+    }
 
     def get_filtered_results(self, filters, handler):
         """Get filtered target results."""

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk/plugins/categories/pre_annotation/actions/to_task.py

@@ -142,7 +142,13 @@ class ToTaskAction(Action):
             'proportion': 100,
         },
     }
-    metrics_categories = {'annotate_task_data'}
+    metrics_categories = {
+        'annotate_task_data': {
+            'stand_by': 0,
+            'failed': 0,
+            'success': 0,
+        }
+    }
 
     def start(self):
         """Start to_task action.
@@ -256,7 +262,9 @@ class ToTaskAction(Action):
         # Process each task
         for task_id in task_ids:
             try:
-                result = self._process_single_task(client, task_id, task_params, target_specification_name)
+                result = self._process_single_task(
+                    client, task_id, task_params, target_specification_name, AnnotationMethod.FILE
+                )
                 if result['success']:
                     success_count += 1
                 else:
@@ -279,7 +287,12 @@ class ToTaskAction(Action):
         self.run.log_message(f'Annotation completed. Success: {success_count}, Failed: {failed_count}')
 
     def _process_single_task(
-        self, client: BackendClient, task_id: int, task_params: Dict[str, Any], target_specification_name: str
+        self,
+        client: BackendClient,
+        task_id: int,
+        task_params: Dict[str, Any],
+        target_specification_name: Optional[str],
+        method: AnnotationMethod,
     ) -> Dict[str, Any]:
         """Process a single task for annotation.
 
@@ -287,7 +300,8 @@ class ToTaskAction(Action):
             client (BackendClient): The backend client instance.
             task_id (int): The task ID to process.
             task_params (Dict[str, Any]): Parameters for getting task data.
-            target_specification_name (str): The name of the target specification.
+            target_specification_name (Optional[str]): The name of the target specification.
+            method (AnnotationMethod): The annotation method to use.
 
         Returns:
             Dict[str, Any]: Result dictionary with 'success' boolean and optional 'error' message.
@@ -308,6 +322,41 @@ class ToTaskAction(Action):
 
         task: Dict[str, Any] = task_response
 
+        if method == AnnotationMethod.FILE:
+            if not target_specification_name:
+                error_msg = 'Target specification name is required for file annotation method'
+                self.run.log_message(f'{error_msg} for task {task_id}')
+                self.run.log_annotate_task_data({'task_id': task_id, 'error': error_msg}, AnnotateTaskDataStatus.FAILED)
+                return {'success': False, 'error': error_msg}
+            return self._process_single_task_with_file(client, task_id, task, target_specification_name)
+        elif method == AnnotationMethod.INFERENCE:
+            return self._process_single_task_with_inference(client, task_id, task)
+        else:
+            error_msg = f'Unsupported annotation method: {method}'
+            self.run.log_message(f'{error_msg} for task {task_id}')
+            self.run.log_annotate_task_data({'task_id': task_id, 'error': error_msg}, AnnotateTaskDataStatus.FAILED)
+            return {'success': False, 'error': error_msg}
+
+    def _process_single_task_with_file(
+        self, client: BackendClient, task_id: int, task: Dict[str, Any], target_specification_name: str
+    ) -> Dict[str, Any]:
+        """Process a single task for file-based annotation.
+
+        Args:
+            client (BackendClient): The backend client instance.
+            task_id (int): The task ID to process.
+            task (Dict[str, Any]): The task data.
+            target_specification_name (str): The name of the target specification.
+
+        Returns:
+            Dict[str, Any]: Result dictionary with 'success' boolean and optional 'error' message.
+        """
+        if not self.run:
+            raise ValueError('Run instance not properly initialized')
+
+        # Type assertion to help the linter
+        assert isinstance(self.run, ToTaskRun)
+
         # Extract data file information
         data_unit = task.get('data_unit', {})
         files = data_unit.get('files', {})
@@ -332,8 +381,12 @@ class ToTaskAction(Action):
             response.raise_for_status()
             data = json.loads(response.content)
 
+            # Convert data to task object
+            annotation_to_task = self.entrypoint(self.run)
+            converted_data = annotation_to_task.convert_data_from_file(data)
+
             # Submit annotation data
-            client.annotate_task_data(task_id, data={'action': 'submit', 'data': data})
+            client.annotate_task_data(task_id, data={'action': 'submit', 'data': converted_data})
 
             # Log success
             self.run.log_annotate_task_data({'task_id': task_id, 'url': url}, AnnotateTaskDataStatus.SUCCESS)
@@ -350,6 +403,84 @@ class ToTaskAction(Action):
             self.run.log_annotate_task_data({'task_id': task_id, 'error': error_msg}, AnnotateTaskDataStatus.FAILED)
             return {'success': False, 'error': error_msg}
 
+    def _process_single_task_with_inference(
+        self, client: BackendClient, task_id: int, task: Dict[str, Any]
+    ) -> Dict[str, Any]:
+        """Process a single task for inference-based annotation.
+
+        Args:
+            client (BackendClient): The backend client instance.
+            task_id (int): The task ID to process.
+            task (Dict[str, Any]): The task data.
+
+        Returns:
+            Dict[str, Any]: Result dictionary with 'success' boolean and optional 'error' message.
+        """
+        if not self.run or not self.params:
+            raise ValueError('Run instance or parameters not properly initialized')
+
+        # Type assertion to help the linter
+        assert isinstance(self.run, ToTaskRun)
+
+        try:
+            # Get pre-processor information
+            pre_processor_id = self.params.get('pre_processor')
+
+            if not pre_processor_id:
+                error_msg = 'Pre-processor ID is required for inference annotation method'
+                self.run.log_message(f'{error_msg} for task {task_id}')
+                self.run.log_annotate_task_data({'task_id': task_id, 'error': error_msg}, AnnotateTaskDataStatus.FAILED)
+                return {'success': False, 'error': error_msg}
+
+            # Call inference pre processor if specified.
+            pre_processor = client.get_plugin_release(pre_processor_id)
+            pre_processor_code = pre_processor['config']['code']
+            pre_processor_version = pre_processor['version']
+
+            # Extract task data for inference
+            data_unit = task.get('data_unit', {})
+            files = data_unit.get('files', {})
+
+            # Find primary image URL from files
+            primary_file_url = ''
+            for file_info in files.values():
+                if file_info.get('is_primary') and file_info.get('url'):
+                    primary_file_url = file_info['url']
+                    break
+
+            pre_processor_params = self.params.get('pre_processor_params', {})
+            pre_processor_params['image_path'] = primary_file_url
+            inference_payload = {
+                'agent': 1,
+                'action': 'inference',
+                'version': pre_processor_version,
+                'params': {
+                    'model': self.params.get('model'),
+                    'method': 'post',
+                    'json': pre_processor_params,
+                },
+            }
+            inference_data = client.run_plugin(pre_processor_code, inference_payload)
+
+            # Convert data to task object
+            annotation_to_task = self.entrypoint(self.run)
+            converted_result = annotation_to_task.convert_data_from_inference(inference_data)
+
+            # Submit inference annotation data
+            client.annotate_task_data(task_id, data={'action': 'submit', 'data': converted_result})
+
+            # Log success
+            self.run.log_annotate_task_data(
+                {'task_id': task_id, 'pre_processor_id': pre_processor_id}, AnnotateTaskDataStatus.SUCCESS
+            )
+            return {'success': True}
+
+        except Exception as e:
+            error_msg = f'Failed to process inference for task {task_id}: {str(e)}'
+            self.run.log_message(error_msg)
+            self.run.log_annotate_task_data({'task_id': task_id, 'error': error_msg}, AnnotateTaskDataStatus.FAILED)
+            return {'success': False, 'error': error_msg}
+
     def _update_metrics(self, total_tasks: int, success_count: int, failed_count: int):
         """Update metrics for task annotation progress.
 
@@ -375,8 +506,53 @@ class ToTaskAction(Action):
         Args:
             task_ids (List[int]): List of task IDs to annotate data to.
         """
-        if not self.run:
-            raise ValueError('Run instance not properly initialized')
+        if not self.run or not self.params:
+            raise ValueError('Run instance or parameters not properly initialized')
 
-        self.run.log_message('Pre annotation with inference is not supported.')
-        self.run.end_log()
+        if not self.params.get('model'):
+            raise ValueError('Model is required for inference annotation method')
+
+        # Type assertion to help the linter
+        assert isinstance(self.run, ToTaskRun)
+        assert isinstance(self.run.client, BackendClient)
+
+        client: BackendClient = self.run.client
+        task_params = {
+            'fields': 'id,data,data_unit',
+            'expand': 'data_unit',
+        }
+
+        total_tasks = len(task_ids)
+        success_count = 0
+        failed_count = 0
+        current_progress = 0
+
+        # Initialize metrics and progress
+        self._update_metrics(total_tasks, success_count, failed_count)
+        self.run.set_progress(0, total_tasks, category='annotate_task_data')
+        self.run.log_message('Annotating data to tasks using inference...')
+
+        # Process each task
+        for task_id in task_ids:
+            try:
+                result = self._process_single_task(client, task_id, task_params, None, AnnotationMethod.INFERENCE)
+                if result['success']:
+                    success_count += 1
+                else:
+                    failed_count += 1
+
+                current_progress += 1
+                self._update_metrics(total_tasks, success_count, failed_count)
+                self.run.set_progress(current_progress, total_tasks, category='annotate_task_data')
+
+            except Exception as e:
+                self.run.log_message(f'Failed to process task {task_id}: {str(e)}')
+                self.run.log_annotate_task_data({'task_id': task_id, 'error': str(e)}, AnnotateTaskDataStatus.FAILED)
+                failed_count += 1
+                current_progress += 1
+                self._update_metrics(total_tasks, success_count, failed_count)
+                self.run.set_progress(current_progress, total_tasks, category='annotate_task_data')
+
+        # Finalize progress
+        self.run.set_progress(total_tasks, total_tasks, category='annotate_task_data')
+        self.run.log_message(f'Inference annotation completed. Success: {success_count}, Failed: {failed_count}')

synapse_sdk-1.0.0a71/synapse_sdk/plugins/categories/pre_annotation/templates/plugin/to_task.py

@@ -0,0 +1,24 @@
+class AnnotationToTask:
+    def __init__(self, run, *args, **kwargs):
+        """Initialize the plugin task pre annotation action class.
+
+        Args:
+            run: Plugin run object.
+        """
+        self.run = run
+
+    def convert_data_from_file(self, data: dict):
+        """Convert the data from a file to a task object.
+
+        Args:
+            data: Converted data.
+        """
+        return data
+
+    def convert_data_from_inference(self, data: dict):
+        """Convert the data from inference result to a task object.
+
+        Args:
+            data: Converted data.
+        """
+        return data

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk/plugins/categories/upload/actions/upload.py

@@ -203,7 +203,18 @@ class UploadAction(Action):
             'proportion': 40,
         },
     }
-    metrics_categories = {'data_file', 'data_unit'}
+    metrics_categories = {
+        'data_file': {
+            'stand_by': 0,
+            'failed': 0,
+            'success': 0,
+        },
+        'data_unit': {
+            'stand_by': 0,
+            'failed': 0,
+            'success': 0,
+        },
+    }
 
     def get_uploader(self, path, file_specification, organized_files):
         """Get uploader from entrypoint."""

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk/plugins/models.py

@@ -128,7 +128,10 @@ class Run:
         self.set_logger()
 
     def set_logger(self):
-        kwargs = {'progress_categories': self.context['progress_categories']}
+        kwargs = {
+            'progress_categories': self.context['progress_categories'],
+            'metrics_categories': self.context['metrics_categories'],
+        }
 
         if self.job_id:
             self.logger = BackendLogger(self.client, self.job_id, **kwargs)

{synapse_sdk-1.0.0a70 → synapse_sdk-1.0.0a71}/synapse_sdk.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synapse-sdk
-Version: 1.0.0a70
+Version: 1.0.0a71
 Summary: synapse sdk
 Author-email: datamaker <developer@datamaker.io>
 License: MIT

synapse_sdk-1.0.0a70/synapse_sdk/plugins/categories/pre_annotation/templates/plugin/to_task.py

@@ -1,8 +0,0 @@
-class AnnotationToTask:
-    def __init__(self, run, *args, **kwargs):
-        """Initialize the plugin task pre annotation action class.
-
-        Args:
-            run: Plugin run object.
-        """
-        self.run = run