added cwl translator

Author: jeff-yc-wong

wfcommons/wfbench/__init__.py

@@ -9,4 +9,4 @@
 # (at your option) any later version.
 
 from .bench import WorkflowBenchmark
-from .translator import DaskTranslator, NextflowTranslator, ParslTranslator, PegasusTranslator, SwiftTTranslator, TaskVineTranslator
+from .translator import DaskTranslator, NextflowTranslator, ParslTranslator, PegasusTranslator, SwiftTTranslator, TaskVineTranslator, CWLTranslator

wfcommons/wfbench/translator/__init__.py

@@ -13,4 +13,5 @@
 from .parsl import ParslTranslator
 from .pegasus import PegasusTranslator
 from .swift_t import SwiftTTranslator
-from .taskvine import TaskVineTranslator
+from .taskvine import TaskVineTranslator
+from .cwl import CWLTranslator

wfcommons/wfbench/translator/cwl.py

@@ -0,0 +1,214 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 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
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+import shutil
+import logging
+import pathlib
+from typing import Union, Optional
+from collections import defaultdict, deque
+
+from .abstract_translator import Translator
+from ...common import Workflow
+
+this_dir = pathlib.Path(__file__).resolve().parent
+
+class CWLTranslator(Translator):
+    """
+    A WfFormat parser for creating CWL workflow benchmarks.
+
+    :param workflow: Workflow benchmark object or path to the workflow benchmark JSON instance.
+    :type workflow: Union[Workflow, pathlib.Path],
+    :param logger: The logger where to log information/warning or errors (optional).
+    :type logger: Logger
+    """
+    def __init__(self,
+                 workflow: Union[Workflow, pathlib.Path],
+                 logger: Optional[logging.Logger] = None) -> None:
+        super().__init__(workflow, logger)
+        self.cwl_script = ["cwlVersion: v1.2",
+                           "class: Workflow",
+                           "requirements:",
+                           "  MultipleInputFeatureRequirement: {}",
+                           "  StepInputExpressionRequirement: {}",
+                           "  InlineJavascriptRequirement: {}"]
+        self.yml_script = []
+        self.parsed_tasks = []
+        self.task_level_map = defaultdict(lambda: [])
+
+        queue = deque(self.root_task_names)
+        visited = set()
+        top_sort = []
+
+        while queue:
+            task_name = queue.popleft()
+
+            if task_name not in visited:
+                top_sort.append(task_name)
+                visited.add(task_name)
+
+            for child in self.task_children[task_name]:
+                queue.append(child)
+
+        assert (len(top_sort) == len(self.tasks))
+
+        levels = {task_name: 0 for task_name in top_sort}
+
+        for task_name in top_sort:
+            for child in self.task_children[task_name]:
+                levels[child] = max(levels[child], levels[task_name] + 1)
+
+        for task_name, level in levels.items():
+            self.task_level_map[level].append(task_name)
+
+    def translate(self, output_folder: pathlib.Path) -> None:
+        # Create output folder
+        output_folder.mkdir(parents=True)
+
+        # Parsing the inputs and outputs of the workflow
+        self._parse_inputs_outputs()
+
+        # Parsing the steos
+        self._parse_steps()
+
+        # additional files
+        self._copy_binary_files(output_folder)
+        self._generate_input_files(output_folder)
+
+        # Writing the CWL files to the output folder
+        self._write_cwl_files(output_folder)
+
+        return 0
+
+    def _parse_steps(self) -> None:
+        steps_folder_source = []
+        self.cwl_script.append("\nsteps:")
+        # Parsing each steps by Workflow levels
+        for level in sorted(self.task_level_map.keys()):
+            # Parsing each task within a Workflow level
+            for task_name in self.task_level_map[level]:
+
+                # Getting the task object
+                task = self.tasks[task_name]
+
+                # Parsing the arguments of the task
+                args_array = []
+                benchmark_name = False
+
+                for item in task.args:
+                    # Split elements that contain both an option and a value
+                    if item.startswith("--"):
+                        parts = item.split(" ", 1)
+                        args_array.append(parts[0])
+                        if len(parts) > 1:
+                            args_array.append(parts[1])
+                    elif not benchmark_name:
+                        args_array.append(item)
+                        benchmark_name = True
+
+                output_files = [
+                    f.file_id for f in task.output_files]
+
+                # Adding the step to the cwl script
+
+                self.cwl_script.append(f"  {task.task_id}:")
+                # TODO: change so that it doesn't only run wfbench programs
+                if not task.program.startswith("wfbench"):
+                    raise ValueError("Only wfbench programs are supported")
+                self.cwl_script.append("    run: clt/wfbench.cwl")
+
+                self.cwl_script.append("    in:")
+                if level == 0:
+                    self.cwl_script.append(
+                        f"      input_files: {task.task_id}_input")
+                else:
+                    self.cwl_script.append(
+                        "      input_files:")
+                    self.cwl_script.append(
+                        "        linkMerge: merge_flattened")
+                    self.cwl_script.append(
+                        "        source:")
+                    for parent in self.task_parents[task_name]:
+                        self.cwl_script.append(
+                            f"          - {parent}/output_files")
+                self.cwl_script.append(
+                    f"      input_params: {{ default: {args_array} }}")
+                self.cwl_script.append("      step_name:")
+                self.cwl_script.append(f"        valueFrom: {task.task_id}")
+                self.cwl_script.append(f"      output_filenames: {{ default: {output_files} }}")
+                self.cwl_script.append(
+                    "    out: [out, err, output_files]\n")
+
+                # Adding a step to create a directory with the output files
+                self.cwl_script.append(f"  {task.task_id}_folder:")
+                self.cwl_script.append("    run: clt/folder.cwl")
+                self.cwl_script.append("    in:")
+                self.cwl_script.append("      - id: item")
+                self.cwl_script.append("        linkMerge: merge_flattened")
+                self.cwl_script.append("        source:")
+                self.cwl_script.append(f"          - {task.task_id}/out")
+                self.cwl_script.append(f"          - {task.task_id}/err")
+                self.cwl_script.append(f"          - {task.task_id}/output_files")
+                self.cwl_script.append("      - id: name")
+                self.cwl_script.append(f"        valueFrom: \"{level}_{task.task_id}\"")
+                self.cwl_script.append("    out: [out]\n")
+
+                # adding the folder id to grand list of step folders
+                steps_folder_source.append(f"{task.task_id}_folder")
+
+        self.cwl_script.append("  final_folder:")
+        self.cwl_script.append("    run: clt/folder.cwl")
+        self.cwl_script.append("    in:")
+        self.cwl_script.append("      - id: item")
+        self.cwl_script.append("        linkMerge: merge_flattened")
+        self.cwl_script.append("        source:")
+        for folder in steps_folder_source:
+            self.cwl_script.append(f"          - {folder}/out")
+        self.cwl_script.append("      - id: name")
+        self.cwl_script.append("        valueFrom: \"final_output\"")
+        self.cwl_script.append("    out: [out]")
+
+    def _parse_inputs_outputs(self) -> None:
+        # Parsing the inputs of all root tasks
+        self.cwl_script.append("\ninputs:")
+        for task_name in self.root_task_names:
+            task = self.tasks[task_name]
+            cwl_written = False
+            yml_written = False
+            for f in task.input_files:
+                if not cwl_written:
+                    self.cwl_script.append(f"  {task.task_id}_input:")
+                    self.cwl_script.append("    type: File[]")
+                    cwl_written = True
+                if not yml_written:
+                    self.yml_script.append(f"{task.task_id}_input:")
+                    yml_written = True
+
+                self.yml_script.append("  - class: File")
+                self.yml_script.append(f"    path: data/{f.file_id}")
+
+        # Appending the output to the cwl script
+        self.cwl_script.append("\noutputs:")
+        self.cwl_script.append("  final_output_folder:")
+        self.cwl_script.append("    type: Directory")
+        self.cwl_script.append("    outputSource: final_folder/out")
+
+    def _write_cwl_files(self, output_folder: pathlib.Path) -> None:
+        cwl_folder = output_folder
+
+        clt_folder = cwl_folder.joinpath("clt")
+        clt_folder.mkdir(exist_ok=True)
+        shutil.copy(pathlib.Path.cwd().joinpath("templates/wfbench.cwl"), clt_folder)
+        shutil.copy(pathlib.Path.cwd().joinpath("templates/folder.cwl"), clt_folder)
+
+        with open(cwl_folder.joinpath("main.cwl"), "w", encoding="utf-8") as f:
+            f.write("\n".join(self.cwl_script))
+
+        with (open(cwl_folder.joinpath("config.yml"), "w", encoding="utf-8")) as f:
+            f.write("\n".join(self.yml_script))

wfcommons/wfbench/translator/templates/cwl_templates/folder.cwl

@@ -0,0 +1,61 @@
+# A collection of RNA-Seq data analysis tools wrapped in CWL scripts
+# Copyright (C) 2019 Alessandro Pio Greco, Patrick Hedley-Miller, Filipe Jesus, Zeyu Yang
+# 
+# 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
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: ExpressionTool
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  item: 
+    type:
+      - File
+      - Directory
+      - type: array
+        items:
+          - File
+          - Directory
+  name: string
+
+outputs:
+    out: Directory
+
+expression: "${
+    if (inputs.item.class == 'Directory'){
+        return {
+            'out': {
+                'class': 'Directory',
+                'basename': inputs.name,
+                'listing': [inputs.item]
+            }
+        }
+    };
+    if (inputs.item.class == 'File'){
+        var arr = [inputs.item];
+        }
+    else {
+        var arr = inputs.item;
+    }
+    return {
+        'out': {
+            'class': 'Directory',
+            'basename': inputs.name,
+            'listing': arr
+        }
+    }
+}"

wfcommons/wfbench/translator/templates/cwl_templates/wfbench.cwl

@@ -0,0 +1,32 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+baseCommand: /Users/wongy/Documents/GitHub/WfFormat-To-StreamFlow-Translator/script/output/bin/wfbench.py
+arguments:
+  - valueFrom: $(inputs.input_params)
+stdout: $(inputs.step_name + ".out")
+stderr: $(inputs.step_name + ".err")
+inputs:
+  step_name:
+    type: string
+  input_params:
+    type: string[]?
+  input_files:
+    type: File[]?
+    inputBinding:
+      position: 0
+  output_filenames:
+    type: string[]?
+outputs:
+  out:
+    type: stdout
+  err:
+    type: stderr
+  output_files:
+    type:
+      type: array
+      items:
+        - File
+    outputBinding:
+      glob: $(inputs.output_filenames)