Support for generating instances with WfFormat 1.5 (closes #43)

wfcommons/common/file.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2023 The WfCommons Team.
+# Copyright (c) 2020-2024 The WfCommons Team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -25,8 +25,8 @@ class FileLink(NoValue):
 class File:
     """Representation of a file.
 
-    :param name: The name of the file.
-    :type name: str
+    :param file_id: The id of the file.
+    :type file_id: str
     :param size: File size in bytes.
     :type size: int
     :param link: Type of file link.
@@ -35,11 +35,11 @@ class File:
     :type logger: Optional[Logger]
     """
 
-    def __init__(self, name: str, size: int, link: FileLink, logger: Optional[Logger] = None) -> None:
+    def __init__(self, file_id: str, size: int, link: FileLink, logger: Optional[Logger] = None) -> None:
         """A file used by tasks."""
         self.logger: Logger = logger if logger else logging.getLogger(__name__)
 
-        self.name: str = name
+        self.file_id: str = file_id
         self.size: int = size
         self.link: FileLink = link
 
@@ -50,7 +50,6 @@ def as_dict(self) -> Dict[str, Union[str, int, FileLink]]:
         :rtype: Dict[str, Union[str, int, FileLink]]
         """
         return {
-            'link': self.link.value,
-            'name': self.name,
+            'id': self.file_id,
             'sizeInBytes': self.size
         }

wfcommons/common/machine.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2023 The WfCommons Team.
+# Copyright (c) 2020-2024 The WfCommons Team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -35,8 +35,9 @@ class Machine:
                 .. code-block:: python
 
                     cpu = {
-                        'count': 48,
-                        'speed': 1200
+                        'coreCount': 48,
+                        'speedInMHz': 1200,
+                        'vendor': 'Vendor Name'
                     }
 
     :type cpu: Dict[str, Union[int, str]]
@@ -73,9 +74,9 @@ def __init__(self,
         self.release: str = release
         self.hashcode = hashcode
 
-        self.cpu_cores: int = cpu['count']
-        self.cpu_speed: int = cpu['speed'] if 'speed' in cpu else 0
-        self.cpu_flops: int = cpu['count'] * cpu['speed'] * 10 ^ 6 if 'speed' in cpu else 0
+        self.cpu_cores: int = cpu['coreCount']
+        self.cpu_speed: int = cpu['speedInMHz'] if 'speedInMHz' in cpu else 0
+        self.cpu_flops: int = cpu['coreCount'] * cpu['speedInMHz'] * 10 ^ 6 if 'speedInMHz' in cpu else 0
         self.cpu_vendor: str = cpu['vendor'] if 'vendor' in cpu else None
 
         self.logger.debug(f"created machine: {self.name} with {self.cpu_cores} cores and {self.cpu_flops} FLOPS.")
@@ -96,9 +97,9 @@ def as_dict(self) -> Dict[str, Union[int, str]]:
         if self.release:
             machine['release'] = self.release
         if self.cpu_cores:
-            machine['cpu'] = {'count': self.cpu_cores}
+            machine['cpu'] = {'coreCount': self.cpu_cores}
         if self.cpu_speed:
-            machine['cpu']['speed'] = self.cpu_speed
+            machine['cpu']['speedInMHz'] = self.cpu_speed
         if self.cpu_vendor:
             machine['cpu']['vendor'] = self.cpu_vendor
         return machine

wfcommons/common/task.py

@@ -31,18 +31,20 @@ class Task:
 
     :param name: The name of the task.
     :type name: str
-    :param task_type: The type of the task.
-    :type task_type: TaskType
+    :param task_id: Task unique ID (e.g., ID0000001).
+    :type task_id: str
     :param runtime: Task runtime in seconds.
     :type runtime: float
+    :param input_files: List of input files used by the task.
+    :type input_files: Optional[List[File]]
+    :param output_files: List of output files used by the task.
+    :type output_files: Optional[List[File]]
     :param cores: Number of cores required by the task.
     :type cores: float
-    :param task_id: Task unique ID (e.g., ID0000001).
-    :type task_id: Optional[str]
     :param category: Task category (can be used, for example, to define tasks that use the same program).
     :type category: Optional[str]
-    :param machine: Machine on which is the task has been executed.
-    :type machine: Optional[Machine]
+    :param machines: Machines on which is the task has been executed.
+    :type machines: Optional[List[Machine]]
     :param program: Program name.
     :type program: Optional[str]
     :param args: List of task arguments.
@@ -61,20 +63,21 @@ class Task:
     :type avg_power: Optional[float]
     :param priority: Task priority.
     :type priority: Optional[int]
-    :param files: List of input/output files used by the task.
-    :type files: Optional[List[File]]
+    :param task_type: The type of the task.
+    :type task_type: TaskType
     :param logger: The logger where to log information/warning or errors.
     :type logger: Optional[Logger]
     """
 
     def __init__(self,
                  name: str,
-                 task_type: TaskType,
+                 task_id: str,
                  runtime: float,
+                 input_files: Optional[List[File]] = None,
+                 output_files: Optional[List[File]] = None,
                  cores: float = 1.0,
-                 task_id: Optional[str] = None,
                  category: Optional[str] = None,
-                 machine: Optional[Machine] = None,
+                 machines: Optional[List[Machine]] = None,
                  program: Optional[str] = None,
                  args: Optional[List[str]] = None,
                  avg_cpu: Optional[float] = None,
@@ -84,19 +87,18 @@ def __init__(self,
                  energy: Optional[int] = None,
                  avg_power: Optional[float] = None,
                  priority: Optional[int] = None,
-                 files: Optional[List[File]] = None,
-                 logger: Optional[Logger] = None,
+                 executedAt: Optional[str] = None,
+                 task_type: Optional[TaskType] = None,
                  launch_dir: Optional[str] = None,
-                 start_time: Optional[str] = None,
+                 logger: Optional[Logger] = None,
                  ) -> None:
         """A task in a workflow."""
         self.logger: Logger = logging.getLogger(
             __name__) if logger is None else logger
         self.name: str = name
-        self.type: TaskType = task_type
+        self.task_id: str = task_id
         self.runtime: float = runtime
         self.cores: Optional[float] = cores
-        self.task_id: Optional[str] = task_id
         self.category: Optional[str] = category
         self.program: Optional[str] = program
         self.args: List[str] = args if args else []
@@ -106,40 +108,45 @@ def __init__(self,
         self.memory: Optional[int] = memory
         self.energy: Optional[int] = energy
         self.avg_power: Optional[float] = avg_power
-        self.files: List[File] = files if files else []
-        self.machine: Machine = machine
+        self.input_files: List[File] = input_files if input_files else []
+        self.output_files: List[File] = output_files if output_files else []
+        self.machines: Optional[List[Machine]] = machines
         self.priority: Optional[int] = priority
+        self.type: Optional[TaskType] = task_type
         self.launch_dir: Optional[str] = launch_dir
-        self.start_time: Optional[str] = str(datetime.now().astimezone().isoformat()) if not start_time else start_time
+        self.start_time: Optional[str] = str(datetime.now().astimezone().isoformat()) if not executedAt else executedAt
         self.logger.debug(
-            f"created {self.type} task {self.name}: runtime => {self.runtime} seconds.")
+            f"created task {self.task_id}: runtime => {self.runtime} seconds.")
 
-    def as_dict(self) -> Dict:
-        """A JSON representation of the task.
+    def specification_as_dict(self) -> Dict:
+        """A JSON representation of the task specification.
 
         :return: A JSON object representation of the task.
         :rtype: Dict
         """
-        task_files = []
-        for f in self.files:
-            task_files.append(f.as_dict())
-
         task_obj = {
             'name': self.name,
-            'type': self.type.value,
-            'command': {},
+            'id': self.task_id,
             'parents': [],
             'children': [],
-            'files': task_files,
+            'input_files': [f.file_id for f in self.input_files],
+            'output_files': [f.file_id for f in self.output_files]
+        }
+        return task_obj
+
+    def execution_as_dict(self) -> Dict:
+        """A JSON representation of the task execution.
+
+        :return: A JSON object representation of the task.
+        :rtype: Dict
+        """
+        task_obj = {
+            'id': self.task_id,
+            'runtimeInSeconds': self.runtime,
+            'command': {}
         }
-        if self.runtime is not None:
-            task_obj['runtimeInSeconds'] = self.runtime
         if self.cores is not None:
-            task_obj['cores'] = self.cores
-        if self.task_id is not None:
-            task_obj['id'] = self.task_id
-        if self.category is not None:
-            task_obj['category'] = self.category
+            task_obj['coreCount'] = self.cores
         if self.avg_cpu is not None:
             task_obj['avgCPU'] = self.avg_cpu
         if self.bytes_read is not None:
@@ -149,19 +156,21 @@ def as_dict(self) -> Dict:
         if self.memory is not None:
             task_obj['memoryInBytes'] = self.memory
         if self.energy is not None:
-            task_obj['energy'] = self.energy
+            task_obj['energyInKWh'] = self.energy
         if self.avg_power is not None:
-            task_obj['avgPower'] = self.avg_power
+            task_obj['avgPowerInKWh'] = self.avg_power
         if self.priority is not None:
             task_obj['priority'] = self.priority
         if self.program is not None:
             task_obj['command']['program'] = self.program
         if self.args is not None:
             task_obj['command']['arguments'] = self.args
-        if self.machine is not None:
-            task_obj['machine'] = self.machine.name
+        if self.machines is not None:
+            task_obj['machines'] = [m.name for m in self.machines]               
+        if self.start_time:
+            task_obj['executedAt'] = self.start_time
+        if self.category is not None:
+            task_obj['category'] = self.category
         if self.launch_dir:
             task_obj['launchDir'] = self.launch_dir
-        if self.start_time:
-            task_obj['startedAt'] = self.start_time
         return task_obj