[med-svn] [Git][med-team/toil][upstream] New upstream version 9.1.2

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch upstream at Debian Med / toil


Commits:
b02ef891 by Michael R. Crusoe at 2026-01-07T14:07:55+01:00
New upstream version 9.1.2
- - - - -


5 changed files:

- src/toil/leader.py
- + src/toil/test/wdl/testfiles/gather.wdl
- src/toil/test/wdl/wdltoil_test.py
- src/toil/wdl/wdltoil.py
- version_template.py


Changes:

=====================================
src/toil/leader.py
=====================================
@@ -349,14 +349,9 @@ class Leader:
     def create_status_sentinel_file(self, fail: bool) -> None:
         """Create a file in the jobstore indicating failure or success."""
         logName = "failed.log" if fail else "succeeded.log"
-        localLog = os.path.join(os.getcwd(), logName)
-        open(localLog, "w").close()
-        self.jobStore.import_file("file://" + localLog, logName, hardlink=True)
-
-        if os.path.exists(
-            localLog
-        ):  # Bandaid for Jenkins tests failing stochastically and unexplainably.
-            os.remove(localLog)
+        with self.jobStore.write_shared_file_stream(logName) as file_handle:
+            # We just need an empty file, so don't write any content
+            pass
 
     def _handledFailedSuccessor(self, successor_id: str, predecessor_id: str) -> bool:
         """


=====================================
src/toil/test/wdl/testfiles/gather.wdl
=====================================
@@ -0,0 +1,52 @@
+version 1.1
+
+workflow gather {
+    input {
+    }
+
+    scatter(number in [1, 2, 3]) {
+        call task1 {
+            input:
+                number=number
+        }
+    }
+
+    call task2 {
+        input:
+            files = task1.foo
+    }
+
+    output {
+        File outfile = task2.outfile
+    }
+}
+
+task task1 {
+
+    input {
+        Int number
+    }
+
+    command <<<
+        echo ~{number} > foo.txt
+    >>>
+
+    output {
+        File foo = "foo.txt"
+    }
+}
+
+task task2 {
+    input {
+        Array[File] files
+    }
+
+    command <<<
+        cat ~{sep=" " files} >out.txt
+    >>>
+
+    output {
+        File outfile = "out.txt"
+    }
+}
+


=====================================
src/toil/test/wdl/wdltoil_test.py
=====================================
@@ -321,6 +321,28 @@ class TestWDL:
 
                 assert "StringFileCoercion.output_file" in result
 
+    @needs_docker
+    def test_gather(self, tmp_path: Path) -> None:
+        """
+        Test files with the same name from different scatter tasks.
+        """
+        with get_data("test/wdl/testfiles/gather.wdl") as wdl:
+            result_json = subprocess.check_output(
+                self.base_command
+                + [
+                    str(wdl),
+                    "-o",
+                    str(tmp_path),
+                    "--logInfo",
+                    "--retryCount=0"
+                ]
+            )
+            result = json.loads(result_json)
+
+            assert "gather.outfile" in result
+            assert isinstance(result["gather.outfile"], str)
+            assert open(result["gather.outfile"]).read() == "1\n2\n3\n"
+
     @needs_docker
     def test_wait(self, tmp_path: Path) -> None:
         """


=====================================
src/toil/wdl/wdltoil.py
=====================================
@@ -5048,6 +5048,9 @@ class WDLSectionJob(WDLBaseJob):
         if subscript is not None:
             # We need to include a scatter loop number.
             task_path += f".{subscript}"
+        # TODO: MyPy can't tell this dict copy will have the same type
+        child_wdl_options = cast(WDLContext, dict(self._wdl_options))
+        child_wdl_options["task_path"] = task_path
 
         if local_environment is not None:
             # Bring local environment into scope
@@ -5115,7 +5118,7 @@ class WDLSectionJob(WDLBaseJob):
                 job: WDLBaseJob = WDLWorkflowNodeJob(
                     section_graph.get(node_ids[0]),
                     rvs,
-                    wdl_options=self._wdl_options,
+                    wdl_options=child_wdl_options,
                     local=True,
                 )
             else:
@@ -5123,7 +5126,7 @@ class WDLSectionJob(WDLBaseJob):
                 job = WDLWorkflowNodeListJob(
                     [section_graph.get(node_id) for node_id in node_ids],
                     rvs,
-                    wdl_options=self._wdl_options,
+                    wdl_options=child_wdl_options,
                     local=True,
                 )
             for prev_job in prev_jobs:
@@ -5158,7 +5161,7 @@ class WDLSectionJob(WDLBaseJob):
             # And to fill in bindings from code not executed in this instantiation
             # with Null, and filter out stuff that should leave scope.
             sink = WDLCombineBindingsJob(
-                leaf_rvs, wdl_options=self._wdl_options, local=True
+                leaf_rvs, wdl_options=child_wdl_options, local=True
             )
             # It runs inside us
             self.addChild(sink)


=====================================
version_template.py
=====================================
@@ -28,7 +28,7 @@ import the expand_ function and invoke it directly with either no or exactly one
 #  - don't import even standard modules at global scope without renaming them
 #    to have leading/trailing underscores
 
-baseVersion = "9.1.0"
+baseVersion = "9.1.2"
 cgcloudVersion = "1.6.0a1.dev393"
 
 



View it on GitLab: https://salsa.debian.org/med-team/toil/-/commit/b02ef8912f816d019c2955a4c4a5ea962624d3c6

-- 
View it on GitLab: https://salsa.debian.org/med-team/toil/-/commit/b02ef8912f816d019c2955a4c4a5ea962624d3c6
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