Merge pull request #113 from inab/full_circle

Full circle 1.0.0b1
inab · Aug 7, 2024 · 571d6b0 · 571d6b0
2 parents e2ac5ea + 43a60cb
commit 571d6b0
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Showing 5 changed files with 7 additions and 5 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -27,5 +27,5 @@ message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/inab/WfExS-backend"
 type: software
 title: "WfExS-backend"
-version: 1.0.0b0
+version: 1.0.0b1
 date-released: "2024-08-07"
diff --git a/wfexs_backend/__init__.py b/wfexs_backend/__init__.py
@@ -21,7 +21,7 @@
 __license__ = "Apache 2.0"
 
 # https://www.python.org/dev/peps/pep-0396/
-__version__ = "1.0.0b0"
+__version__ = "1.0.0b1"
 __url__ = "https://github.com/inab/WfExS-backend"
 __official_name__ = "WfExS-backend"
 

diff --git a/wfexs_backend/utils/contents.py b/wfexs_backend/utils/contents.py
@@ -282,7 +282,7 @@ def CWLDesc2Content(
             )
         elif foundKind == ContentKind.File:
             matValue = GeneratedContent(
-                local=cwlDesc["path"],
+                local=pathlib.Path(cwlDesc["path"]),
                 signature=cast(
                     "Fingerprint",
                     ComputeDigestFromFile(cwlDesc["path"], repMethod=repMethod),

diff --git a/wfexs_backend/workflow.py b/wfexs_backend/workflow.py
@@ -4876,11 +4876,12 @@ def _unmarshallExecuteFH(
             if job_status in (ExecutionStatus.Queued, ExecutionStatus.Running):
                 try:
                     job_id = int(execution.get("job_id", ""))
-                    queued = datetime.datetime.fromtimestamp(
+                    queued_proc = datetime.datetime.fromtimestamp(
                         psutil.Process(job_id).create_time()
                     ).astimezone()
 
-                    if queued != execution.get("queued", datetime.datetime.min):
+                    queued = execution.get("queued", datetime.datetime.min)
+                    if queued_proc != queued:
                         job_status = ExecutionStatus.Died
                 except (psutil.NoSuchProcess, ValueError, TypeError):
                     job_status = ExecutionStatus.Died

diff --git a/wfexs_backend/workflow_engines/cwl_engine.py b/wfexs_backend/workflow_engines/cwl_engine.py
@@ -1385,6 +1385,7 @@ def launchWorkflow(
                             started = datetime.datetime.now().astimezone()
                             yield StagedExecution(
                                 status=ExecutionStatus.Running,
+                                job_id=str(os.getpid()),
                                 exitVal=cast("ExitVal", -1),
                                 augmentedInputs=augmentedInputs,
                                 # TODO: store the augmentedEnvironment instead