[arvados] created: 2.1.0-2887-g43d62a887
git repository hosting
git at public.arvados.org
Mon Sep 12 13:35:47 UTC 2022
at 43d62a887fbe06d21c9976c2d87e5ec93bf37dae (commit)
commit 43d62a887fbe06d21c9976c2d87e5ec93bf37dae
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Sun Sep 11 23:05:37 2022 -0400
19425: Set loadingContext.skip_resolve_all
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 36be733d7..0c2276bd6 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -615,7 +615,7 @@ The 'jobs' API is no longer supported.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
- loadingContext.codegen_idx = {}
+ loadingContext.skip_resolve_all = True
with Perf(metrics, "load_tool"):
tool = load_tool(tool.tool, loadingContext)
commit b1de74951cd6203dd23a5c9985331e36742f2502
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Sun Sep 11 22:07:50 2022 -0400
19425: Clear codegen_idx before reloading
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 8635d5fcf..36be733d7 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -611,10 +611,11 @@ The 'jobs' API is no longer supported.
# Recreate process object (ArvadosWorkflow or
# ArvadosCommandTool) because tool document may have been
# updated by upload_workflow_deps in ways that modify
- # inheritance of hints or requirements.
+ # hints or requirements.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
+ loadingContext.codegen_idx = {}
with Perf(metrics, "load_tool"):
tool = load_tool(tool.tool, loadingContext)
commit f20bfeeafe87304531c77875c68d9333849f570a
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Sat Sep 10 12:29:51 2022 -0400
19425: Fix passing --fast-parser
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 0f3f67537..1c3eca5e4 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -586,7 +586,7 @@ class RunnerContainer(Runner):
if runtimeContext.enable_preemptible is False:
command.append("--disable-preemptible")
- if runtimeContext.fast_parser:
+ if self.fast_parser:
command.append("--fast-parser")
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 225f4ae60..d92dd8f21 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -823,6 +823,7 @@ class Runner(Process):
self.priority = priority
self.secret_store = secret_store
self.enable_dev = loadingContext.enable_dev
+ self.fast_parser = loadingContext.fast_parser
self.submit_runner_cores = 1
self.submit_runner_ram = 1024 # defaut 1 GiB
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 0448e9f7a..3f7bc26bd 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,7 +36,7 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220909193950',
+ 'cwltool==3.1.20220910163051',
'schema-salad==8.3.20220825114525',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
commit 84c2931f331735f94b08e746ad9d3fd2782b6010
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Fri Sep 9 17:09:55 2022 -0400
19425: cwltool dev
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 f576b973d..0448e9f7a 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,7 +36,7 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220909192237',
+ 'cwltool==3.1.20220909193950',
'schema-salad==8.3.20220825114525',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
commit 3f424be8b9f5c4c10296a6b78b6f4dff1cc51f84
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Fri Sep 9 15:26:43 2022 -0400
19425: cwltool dev version bump
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 5094ea3bf..0f3f67537 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -586,6 +586,9 @@ class RunnerContainer(Runner):
if runtimeContext.enable_preemptible is False:
command.append("--disable-preemptible")
+ if runtimeContext.fast_parser:
+ command.append("--fast-parser")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index d87012438..f576b973d 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,7 +36,7 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220909180746',
+ 'cwltool==3.1.20220909192237',
'schema-salad==8.3.20220825114525',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
commit 457bb9b45c91645518ad9001c1b46addde7a4c47
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Fri Sep 9 14:16:44 2022 -0400
19425: Add experimental --fast-parser
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 08a05d571..c88cb66a6 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -207,6 +207,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
action="store_true", default=False,
help=argparse.SUPPRESS)
+ parser.add_argument("--fast-parser", dest="fast_parser",
+ action="store_true", default=False,
+ help=argparse.SUPPRESS)
+
parser.add_argument("--thread-count", type=int,
default=0, help="Number of threads to use for job submit and output collection.")
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index ef0980ae5..d87012438 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,7 +36,7 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220907141119',
+ 'cwltool==3.1.20220909180746',
'schema-salad==8.3.20220825114525',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
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