From f4e1c5c2320a157d2a167b12b91fcaba3f8a29ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20M=C2=AA=20Fern=C3=A1ndez?=
 <jose.m.fernandez@bsc.es>
Date: Wed, 7 Aug 2024 22:27:49 +0200
Subject: [PATCH 1/3] Fixed corner case where a string path from a CWL workflow
 was used instead of a pathlib.Path instance

---
 wfexs_backend/utils/contents.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wfexs_backend/utils/contents.py b/wfexs_backend/utils/contents.py
index 7b5a960..9ec3763 100644
--- 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),

From 09054706b3969e3ebec4f30b16c1235ea657468e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20M=C2=AA=20Fern=C3=A1ndez?=
 <jose.m.fernandez@bsc.es>
Date: Wed, 7 Aug 2024 23:07:03 +0200
Subject: [PATCH 2/3] Fixed corner case where a running CWL job was not
 registering its PID as job_id

---
 wfexs_backend/workflow.py                    | 5 +++--
 wfexs_backend/workflow_engines/cwl_engine.py | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/wfexs_backend/workflow.py b/wfexs_backend/workflow.py
index e7a525d..a2c3b2f 100644
--- 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
index f7cae92..75f48da 100644
--- 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

From 43a60cbc4841a16fb1b781145a7974def7c5da33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20M=C2=AA=20Fern=C3=A1ndez?=
 <jose.m.fernandez@bsc.es>
Date: Wed, 7 Aug 2024 23:09:23 +0200
Subject: [PATCH 3/3] Version bump to 1.0.0b1

---
 CITATION.cff              | 2 +-
 wfexs_backend/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 811677b..9f4bb00 100644
--- 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
index f15da79..e26a8b3 100644
--- 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"