Fixed tag hierarchy check (#670)

This commit introduces a proper way to check if a `Token` derives from another
`Token` based on their tags. Before this commit, tags were compared using the
`startswith` method of the `str` class. However, this could lead to incorrect results
because tags are represented by numbers. Now, a dedicated `_is_parent_tag`
method has been introduced.

Co-authored-by: GlassOfWhiskey <[email protected]>

streamflow/cwl/utils.py

@@ -709,7 +709,7 @@ def process_embedded_tool(
     step_name: str,
     name_prefix: str,
     context: MutableMapping[str, Any],
-):
+) -> tuple[cwl_utils.parser.Process, str, MutableMapping[str, Any]]:
     run_command = cwl_element.run
     inner_context = dict(context)
     # If the `run` options contains an inline CWL object
@@ -740,7 +740,7 @@ def process_embedded_tool(
             )
     # Otherwise, the `run` options contains an URI
     else:
-        # Fetch and translare the target file
+        # Fetch and translate the target file
         run_command = cwl_utils.parser.load_document_by_uri(
             path=cwl_element.loadingOptions.fetcher.urljoin(
                 base_url=cwl_element.loadingOptions.fileuri, url=run_command

streamflow/workflow/step.py

@@ -44,6 +44,25 @@ def _get_directory(path_processor: ModuleType, directory: str | None, target: Ta
     return directory or path_processor.join(target.workdir, utils.random_name())
 
 
+def _get_token_ids(token_list):
+    return [t.persistent_id for t in (token_list or []) if t.persistent_id]
+
+
+def _group_by_tag(
+    inputs: MutableMapping[str, Token],
+    inputs_map: MutableMapping[str, MutableMapping[str, Token]],
+) -> None:
+    for name, token in inputs.items():
+        if token.tag not in inputs_map:
+            inputs_map[token.tag] = {}
+        inputs_map[token.tag][name] = token
+
+
+def _is_parent_tag(tag: str, parent: str) -> bool:
+    parent_idx = parent.split(".")
+    return tag.split(".")[: len(parent_idx)] == parent_idx
+
+
 def _reduce_statuses(statuses: MutableSequence[Status]):
     num_skipped = 0
     for status in statuses:
@@ -59,20 +78,6 @@ def _reduce_statuses(statuses: MutableSequence[Status]):
         return Status.COMPLETED
 
 
-def _group_by_tag(
-    inputs: MutableMapping[str, Token],
-    inputs_map: MutableMapping[str, MutableMapping[str, Token]],
-) -> None:
-    for name, token in inputs.items():
-        if token.tag not in inputs_map:
-            inputs_map[token.tag] = {}
-        inputs_map[token.tag][name] = token
-
-
-def _get_token_ids(token_list):
-    return [t.persistent_id for t in (token_list or []) if t.persistent_id]
-
-
 class BaseStep(Step, ABC):
     def __init__(self, name: str, workflow: Workflow):
         super().__init__(name, workflow)
@@ -250,9 +255,9 @@ def _add_to_list(
         for key in list(self._token_values.keys()):
             if tag == key:
                 continue
-            elif key.startswith(tag):
+            elif _is_parent_tag(key, tag):
                 self._add_to_port(token, self._token_values[key], port_name)
-            elif tag.startswith(key):
+            elif _is_parent_tag(tag, key):
                 if tag not in self._token_values:
                     self._token_values[tag] = {}
                 for p in self._token_values[key]:

tests/test_remotepath.py

@@ -155,7 +155,7 @@ async def test_mkdir_failure(context):
     with pytest.raises(WorkflowExecutionException) as err:
         await path.mkdir(mode=mode)
     expected_msg_err = f"1 Command 'mkdir -m {mode:o} {path}' on location {location}: mkdir: can't create directory '{path}': File exists"
-    assert str(err.value) == expected_msg_err
+    assert expected_msg_err in str(err.value)
 
 
 @pytest.mark.asyncio