Fixed bugs in dot-file handling in the Workflow class

Added testing

Author: henricasanova

.github/workflows/build.yml

@@ -27,7 +27,9 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install stress-ng
+          sudo apt-get install graphviz libgraphviz-dev
           pip install docker
+          pip install graphviz
 
       - name: Check package install
         run: |

tests/unit/common/test_workflow.py

@@ -140,7 +140,37 @@ def test_workflow_json_generation(self):
         # Compare the two jsons!
         assert(original_json == written_json)
 
+    @pytest.mark.unit
+    def test_workflow_dot_file(self):
+
+        # Put a JSON file in /tmp
+        url = "https://raw.githubusercontent.com/wfcommons/WfInstances/refs/heads/main/makeflow/blast/blast-chameleon-small-001.json"
+        response = requests.get(url)
+        local_file_name = url.split("/")[-1]
+        with open("/tmp/" + local_file_name, 'wb') as f:
+            f.write(response.content)
+
+        # Create an instance from the JSON File and write it back to a JSON
+        instance = Instance(pathlib.Path("/tmp") / local_file_name)
 
+        # Capture some metrics
+        num_tasks = len(instance.workflow.tasks)
+        num_dependencies = len(instance.workflow.edges)
+
+        # # Create a dot file
+        dot_path = pathlib.Path("/tmp/written_workflow.dot")
+        instance.workflow.write_dot(dot_path)
+        assert dot_path.exists()
+        with open(str(dot_path), "r", encoding="utf-8") as f:
+            content = f.read()
+            assert(num_tasks == content.count("label") - 1)  # Extra "label" in file for \N
+            assert(num_dependencies == content.count("->"))  # Extra "label" in file for \N
+
+        # Read it back
+        instance.workflow.read_dot(dot_path)
+        assert(num_tasks == len(instance.workflow.tasks))
+        assert(num_tasks == len(instance.workflow.nodes))
+        assert(num_dependencies == len(instance.workflow.edges))
 
 
 

wfcommons/common/workflow.py

@@ -236,7 +236,14 @@ def read_dot(self, dot_file_path: Optional[pathlib.Path] = None) -> None:
             raise ModuleNotFoundError(
                 f"\'pydot\' package not found: call to {type(self).__name__}.read_dot() failed.")
 
-        graph = nx.drawing.nx_pydot.read_dot(dot_file_path)
+        # graph = nx.drawing.nx_pydot.read_dot(str(dot_file_path))
+        graph = nx.nx_agraph.read_dot(str(dot_file_path))
+
+        # clear everything
+        self.tasks.clear()
+        self.tasks_parents.clear()
+        self.tasks_children.clear()
+        self.clear()
 
         tasks_map = {}
         for node in graph.nodes(data=True):

wfcommons/wfchef/recipes/blast/recipe.py

@@ -39,7 +39,7 @@ class BlastRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/bwa/recipe.py

@@ -39,7 +39,7 @@ class BwaRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/cycles/recipe.py

@@ -39,7 +39,7 @@ class CyclesRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/epigenomics/recipe.py

@@ -39,7 +39,7 @@ class EpigenomicsRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/genome/recipe.py

@@ -39,7 +39,7 @@ class GenomeRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/montage/recipe.py

@@ -39,7 +39,7 @@ class MontageRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,

wfcommons/wfchef/recipes/rnaseq/recipe.py

@@ -39,7 +39,7 @@ class RnaseqRecipe(WfChefWorkflowRecipe):
     def __init__(self,
                  data_footprint: Optional[int] = 0,
                  num_tasks: Optional[int] = 3,
-                 exclude_graphs: Set[str] = None,
+                 exclude_graphs: Set[str]|None = None,
                  runtime_factor: Optional[float] = 1.0,
                  input_file_size_factor: Optional[float] = 1.0,
                  output_file_size_factor: Optional[float] = 1.0,