Allow for newer pydot version (#2019)

Co-authored-by: "FeRD (Frank Dana)" <[email protected]>
Co-authored-by: Michael R. Crusoe <[email protected]>

Author: 3 people

cwltool/cwlviewer.py

@@ -99,8 +99,8 @@ def _set_inner_edges(self) -> None:
             self._dot_graph.add_node(n)
             self._dot_graph.add_edge(
                 pydot.Edge(
-                    str(inner_edge_row["source_step"]),
-                    str(inner_edge_row["target_step"]),
+                    pydot.quote_id_if_necessary(str(inner_edge_row["source_step"])),
+                    pydot.quote_id_if_necessary(str(inner_edge_row["target_step"])),
                 )
             )
 
@@ -109,7 +109,6 @@ def _set_input_edges(self) -> None:
         inputs_subgraph = pydot.Subgraph(graph_name="cluster_inputs")
         self._dot_graph.add_subgraph(inputs_subgraph)
         inputs_subgraph.set("rank", "same")
-        inputs_subgraph.create_attribute_methods(["style"])
         inputs_subgraph.set("style", "dashed")
         inputs_subgraph.set("label", "Workflow Inputs")
 
@@ -129,14 +128,18 @@ def _set_input_edges(self) -> None:
             )
             n.set_name(str(input_row["input"]))
             inputs_subgraph.add_node(n)
-            self._dot_graph.add_edge(pydot.Edge(str(input_row["input"]), str(input_row["step"])))
+            self._dot_graph.add_edge(
+                pydot.Edge(
+                    pydot.quote_id_if_necessary(str(input_row["input"])),
+                    pydot.quote_id_if_necessary(str(input_row["step"])),
+                )
+            )
 
     def _set_output_edges(self) -> None:
         get_output_edges = _get_output_edges_query()
         outputs_graph = pydot.Subgraph(graph_name="cluster_outputs")
         self._dot_graph.add_subgraph(outputs_graph)
         outputs_graph.set("rank", "same")
-        outputs_graph.create_attribute_methods(["style"])
         outputs_graph.set("style", "dashed")
         outputs_graph.set("label", "Workflow Outputs")
         outputs_graph.set("labelloc", "b")
@@ -156,7 +159,12 @@ def _set_output_edges(self) -> None:
             )
             n.set_name(str(output_edge_row["output"]))
             outputs_graph.add_node(n)
-            self._dot_graph.add_edge(pydot.Edge(output_edge_row["step"], output_edge_row["output"]))
+            self._dot_graph.add_edge(
+                pydot.Edge(
+                    pydot.quote_id_if_necessary(output_edge_row["step"]),
+                    pydot.quote_id_if_necessary(output_edge_row["output"]),
+                )
+            )
 
     def _get_root_graph_uri(self) -> rdflib.term.Identifier:
         get_root_query = _get_root_query()

mypy-stubs/pydot.pyi

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Sequence, Union
+from typing import Any, Dict, List, Optional, Sequence, Union
 
 PY3: Any
 str_type = str
@@ -12,6 +12,7 @@ def is_windows() -> bool: ...
 def is_anaconda() -> bool: ...
 def get_executable_extension() -> str: ...
 def graph_from_dot_data(s: str) -> List["Dot"]: ...
+def quote_id_if_necessary(s: str, unquoted_keywords: Optional[Sequence[str]] = None) -> str: ...
 
 class Common:
     def set_parent_graph(self, parent_graph: "Graph") -> None: ...
@@ -21,7 +22,6 @@ class Common:
     def get_attributes(self) -> Dict[str, str]: ...
     def set_sequence(self, seq: str) -> None: ...
     def get_sequence(self) -> str: ...
-    def create_attribute_methods(self, obj_attributes: List[str]) -> None: ...
 
 class Error(Exception):
     value: Any

requirements.txt

@@ -7,7 +7,7 @@ mypy-extensions
 psutil>=5.6.6
 importlib_resources>=1.4;python_version<'3.9'
 coloredlogs
-pydot>=1.4.1,<3
+pydot>=1.4.1
 argcomplete>=1.12.0
 pyparsing!=3.0.2  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
 cwl-utils>=0.32

setup.py

@@ -156,7 +156,7 @@ def _find_package_data(base: str, globs: list[str], root: str = "cwltool") -> li
         "mypy-extensions",
         "psutil >= 5.6.6",
         "coloredlogs",
-        "pydot >= 1.4.1, <3",
+        "pydot >= 1.4.1",
         "argcomplete >= 1.12.0",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
         "cwl-utils >= 0.32",

tests/test_context.py

@@ -1,10 +1,10 @@
 import logging
 import subprocess
 import sys
+from collections.abc import MutableMapping
 from io import StringIO
 from pathlib import Path
 from typing import cast
-from collections.abc import MutableMapping
 
 from cwltool.context import RuntimeContext
 from cwltool.factory import Factory