[arvados] created: 2.1.0-3015-ga2596809a
git repository hosting
git at public.arvados.org
Wed Nov 2 02:07:22 UTC 2022
at a2596809a623bfcc34d53e68b58c401b5393ef36 (commit)
commit a2596809a623bfcc34d53e68b58c401b5393ef36
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Sep 13 16:50:09 2022 -0400
19425: Bump to released cwltool & schema-salad
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 6fb804045..2bef1f3cd 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,8 +36,8 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220910163051',
- 'schema-salad==8.3.20220825114525',
+ 'cwltool==3.1.20220913185150',
+ 'schema-salad==8.3.20220913105718',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
'ciso8601 >= 2.0.0',
commit 66f0a7865d34d2599eb3ef56f22023119c0f500b
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 bf6ec8d0f..434f63c4e 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -691,7 +691,7 @@ 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 0ed081dcde1e771157d22659519207877ad535e2
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 f95ac17e1..bf6ec8d0f 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -687,10 +687,11 @@ 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 8d34b283a37ada425152221003c348e2f6267f6c
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 f5373c4e3..86f1e24f0 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -604,7 +604,7 @@ 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 486103919..25c7eaf6c 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -843,6 +843,7 @@ class Runner(Process):
self.secret_store = secret_store
self.enable_dev = loadingContext.enable_dev
self.git_info = git_info
+ 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 8f0b6eb73..6fb804045 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 35127771fadae046acf212cbed964a6c507dc004
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 8196f91b4..8f0b6eb73 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 9cf87cec431ea1f48a633da284cbb2461e3cd056
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 57ab7367a..f5373c4e3 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -604,6 +604,9 @@ 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 4c4163e48..8196f91b4 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 007498822ee29bfcf298861bdc19b716471232d2
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 9200c5caa..19951327f 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 33c1ffcbf..4c4163e48 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,8 +36,8 @@ setup(name='arvados-cwl-runner',
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==3.1.20220907141119',
- 'schema-salad==8.3.20220913105718',
+ 'cwltool==3.1.20220909180746',
+ 'schema-salad==8.3.20220825114525',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
'ciso8601 >= 2.0.0',
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