[arvados] created: 2.7.0-6526-g8677b41d05

[git repository hosting]

        at  8677b41d05edea3f4b1fad8d662a519ee81e196d (commit)


commit 8677b41d05edea3f4b1fad8d662a519ee81e196d
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon May 13 11:13:43 2024 -0400

    21718: Update cwltool dependency -- currently unreleased
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 5d8486f64f..d56ff4d2ae 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -29,8 +29,8 @@ setup(name='arvados-cwl-runner',
       # build.
       install_requires=[
           *arvados_version.iter_dependencies(version),
-          'cwltool==3.1.20230601100705',
-          'schema-salad==8.4.20230601112322',
+          'cwltool==3.1.20240404144622.dev7+g270f9c6c',
+          'schema-salad==8.5.20240410123758',
           'ciso8601 >= 2.0.0',
           'setuptools>=40.3.0',
       ],

commit ec45472536ba42e10d58f26a2b09e948ac45a6c8
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue May 7 09:11:14 2024 -0400

    21718: Remove unused import
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 0cd6295fbb..c80a4b3f2f 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -31,11 +31,6 @@ from typing import (
     Union,
     cast,
 )
-from cwltool.utils import (
-    CWLObjectType,
-    CWLOutputAtomType,
-    CWLOutputType,
-)
 
 import subprocess
 

commit 582431f2410ed43351aca54363a401eb365191a5
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri May 3 10:38:19 2024 -0400

    21718: Replace .decode method with str(bytes, "utf-8")
    
    This is because some bytes-like objects (such as memoryview) don't
    have a "decode()" method. It appears that the preferred way to get a
    decoded string is to simply call the constructor with the bytes-like
    object and the desired encoding.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvdocker.py b/sdk/cwl/arvados_cwl/arvdocker.py
index f5e67a6649..ae5a434074 100644
--- a/sdk/cwl/arvados_cwl/arvdocker.py
+++ b/sdk/cwl/arvados_cwl/arvdocker.py
@@ -19,11 +19,10 @@ logger = logging.getLogger('arvados.cwl-runner')
 
 def determine_image_id(dockerImageId):
     for line in (
-        subprocess.check_output(  # nosec
-            ["docker", "images", "--no-trunc", "--all"]
-        )
-        .decode("utf-8")
-        .splitlines()
+            str(subprocess.check_output(  # nosec
+                ["docker", "images", "--no-trunc", "--all"]
+            ), "utf-8")
+            .splitlines()
     ):
         try:
             match = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", line)
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index dae68459bc..4751e48c04 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -317,7 +317,7 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid,
 
         text = tool.doc_loader.fetch_text(w)
         if isinstance(text, bytes):
-            textIO = StringIO(text.decode('utf-8'))
+            textIO = StringIO(str(text, 'utf-8'))
         else:
             textIO = StringIO(text)
 
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 259294a36e..0cd6295fbb 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -929,7 +929,7 @@ class Runner(Process):
             if "cwl.output.json" in outc:
                 with outc.open("cwl.output.json", "rb") as f:
                     if f.size() > 0:
-                        outputs = json.loads(f.read().decode())
+                        outputs = json.loads(str(f.read(), 'utf-8'))
             def keepify(fileobj):
                 path = fileobj["location"]
                 if not path.startswith("keep:"):

-----------------------------------------------------------------------


hooks/post-receive
--