[arvados] updated: 2.6.0-34-g59ffa1048
git repository hosting
git at public.arvados.org
Wed Apr 19 20:59:34 UTC 2023
Summary of changes:
sdk/cwl/arvados_cwl/__init__.py | 7 +++++++
sdk/cwl/arvados_cwl/executor.py | 10 ++++++++--
sdk/python/arvados/http_import.py | 7 ++++++-
3 files changed, 21 insertions(+), 3 deletions(-)
via 59ffa1048ea27cfc18dfb510868edd994c0af5b2 (commit)
via 63415c0ba76d02d2c60e905fac71c09f381af275 (commit)
via be502b6f72f839b8af7660f02a6a289de0b7876e (commit)
via e8051f365b74077b570e7ba47576da5ca25fea2f (commit)
via 8c8f10692679395046e76c5fc6c8d95733c71232 (commit)
from 7f545f1feabcb30fa0ccb3cab3f46392d01f0fea (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 59ffa1048ea27cfc18dfb510868edd994c0af5b2
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Apr 19 16:59:16 2023 -0400
20257: Don't log arvados.keep at INFO
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 7ab612c82..63df4db7a 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -358,6 +358,7 @@ def main(args=sys.argv[1:],
# show up.
logger.setLevel(logging.INFO)
logging.getLogger('arvados').setLevel(logging.INFO)
+ logging.getLogger('arvados.keep').setLevel(logging.WARNING)
if arvargs.debug:
logger.setLevel(logging.DEBUG)
commit 63415c0ba76d02d2c60e905fac71c09f381af275
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Apr 19 16:43:17 2023 -0400
20257: Set INFO log level explicitly
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 74ca9312b..7ab612c82 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -353,6 +353,12 @@ def main(args=sys.argv[1:],
# Note that unless in debug mode, some stack traces related to user
# workflow errors may be suppressed.
+
+ # For some reason if I don't set these explicitly some logs won't
+ # show up.
+ logger.setLevel(logging.INFO)
+ logging.getLogger('arvados').setLevel(logging.INFO)
+
if arvargs.debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
diff --git a/sdk/python/arvados/http_import.py b/sdk/python/arvados/http_import.py
index a88084e9d..91185d974 100644
--- a/sdk/python/arvados/http_import.py
+++ b/sdk/python/arvados/http_import.py
@@ -232,7 +232,9 @@ def etag_quote(etag):
return '"' + etag + '"'
-def http_to_keep(api, project_uuid, url, utcnow=datetime.datetime.utcnow, varying_url_params="", prefer_cached_downloads=False):
+def http_to_keep(api, project_uuid, url,
+ utcnow=datetime.datetime.utcnow, varying_url_params="",
+ prefer_cached_downloads=False):
logger.info("Checking Keep for %s", url)
commit be502b6f72f839b8af7660f02a6a289de0b7876e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Apr 19 16:08:39 2023 -0400
20257: Add message before doing any HTTP activity
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/python/arvados/http_import.py b/sdk/python/arvados/http_import.py
index f4913a5b7..a88084e9d 100644
--- a/sdk/python/arvados/http_import.py
+++ b/sdk/python/arvados/http_import.py
@@ -233,6 +233,9 @@ def etag_quote(etag):
def http_to_keep(api, project_uuid, url, utcnow=datetime.datetime.utcnow, varying_url_params="", prefer_cached_downloads=False):
+
+ logger.info("Checking Keep for %s", url)
+
varying_params = [s.strip() for s in varying_url_params.split(",")]
parsed = urllib.parse.urlparse(url)
commit e8051f365b74077b570e7ba47576da5ca25fea2f
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Apr 19 15:44:11 2023 -0400
20257: Tweak runtime status for 'activity'
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 92894b36c..22e3f1fde 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -281,7 +281,7 @@ The 'jobs' API is no longer supported.
runtime_status = current.get('runtime_status', {})
original_updatemessage = updatemessage = runtime_status.get(kind, "")
- if not updatemessage:
+ if kind == "activity" or not updatemessage:
updatemessage = message
# Subsequent messages tacked on in detail
commit 8c8f10692679395046e76c5fc6c8d95733c71232
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Apr 19 15:18:44 2023 -0400
20257: Record basic workflow status in "activity"
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 ef84dd498..92894b36c 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -266,7 +266,7 @@ The 'jobs' API is no longer supported.
activity statuses, for example in the RuntimeStatusLoggingHandler.
"""
- if kind not in ('error', 'warning'):
+ if kind not in ('error', 'warning', 'activity'):
# Ignore any other status kind
return
@@ -593,6 +593,8 @@ The 'jobs' API is no longer supported.
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
+ self.runtime_status_update("activity", "initialization")
+
git_info = self.get_git_info(updated_tool) if self.git_info else {}
if git_info:
logger.info("Git provenance")
@@ -655,6 +657,8 @@ The 'jobs' API is no longer supported.
self.project_uuid = runtimeContext.project_uuid
+ self.runtime_status_update("activity", "data transfer")
+
# Upload local file references in the job order.
with Perf(metrics, "upload_job_order"):
job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name,
@@ -823,6 +827,8 @@ The 'jobs' API is no longer supported.
# We either running the workflow directly, or submitting it
# and will wait for a final result.
+ self.runtime_status_update("activity", "workflow execution")
+
current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
if current_container:
logger.info("Running inside container %s", current_container.get("uuid"))
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