[ARVADOS] created: 1.3.0-3191-g7850378a1
Git user
git at public.arvados.org
Mon Sep 21 19:55:33 UTC 2020
at 7850378a1ffb342fba2ba197370e17d1b777326f (commit)
commit 7850378a1ffb342fba2ba197370e17d1b777326f
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Mon Sep 21 14:44:57 2020 -0400
16856: Log the cluster being submitted to
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/apps/workbench/app/views/work_units/_show_component.html.erb b/apps/workbench/app/views/work_units/_show_component.html.erb
index cac263d1e..4cce090a2 100644
--- a/apps/workbench/app/views/work_units/_show_component.html.erb
+++ b/apps/workbench/app/views/work_units/_show_component.html.erb
@@ -45,13 +45,13 @@ SPDX-License-Identifier: AGPL-3.0 %>
<div class="panel-heading">
<h4 class="panel-title">
<a class="component-detail-panel" data-toggle="collapse" href="#errorDetail">
- <span class="caret"></span> Error: <%= sanitize(wu.runtime_status[:error]) %>
+ <span class="caret"></span> Error: <%= h(wu.runtime_status[:error]) %>
</a>
</h4>
</div>
<div id="errorDetail" class="panel-body panel-collapse collapse">
<% if wu.runtime_status[:errorDetail] %>
- <pre><%= sanitize(wu.runtime_status[:errorDetail]) %></pre>
+ <pre><%= h(wu.runtime_status[:errorDetail]) %></pre>
<% else %>
No detailed information available.
<% end %>
@@ -69,13 +69,13 @@ SPDX-License-Identifier: AGPL-3.0 %>
<div class="panel-heading">
<h4 class="panel-title">
<a class="component-detail-panel" data-toggle="collapse" href="#warningDetail">
- <span class="caret"></span> Warning: <%= sanitize(wu.runtime_status[:warning]) %>
+ <span class="caret"></span> Warning: <%= h(wu.runtime_status[:warning]) %>
</a>
</h4>
</div>
<div id="warningDetail" class="panel-body panel-collapse collapse">
<% if wu.runtime_status[:warningDetail] %>
- <pre><%= sanitize(wu.runtime_status[:warningDetail]) %></pre>
+ <pre><%= h(wu.runtime_status[:warningDetail]) %></pre>
<% else %>
No detailed information available.
<% end %>
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 9d14ceeab..99d82f339 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -325,8 +325,8 @@ class ArvadosContainer(JobBase):
logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
else:
logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
- except Exception:
- logger.exception("%s got an error", self.arvrunner.label(self))
+ except Exception as e:
+ logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
logger.debug("Container request was %s", container_request)
self.output_callback({}, "permanentFail")
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 9ba798ec6..68141586d 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -524,6 +524,8 @@ The 'jobs' API is no longer supported.
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
+ logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], self.api.config()["Services"]["Controller"]["ExternalURL"])
+
updated_tool.visit(self.check_features)
self.project_uuid = runtimeContext.project_uuid
diff --git a/sdk/dev-jobs.dockerfile b/sdk/dev-jobs.dockerfile
index dd067e977..f7719dbc4 100644
--- a/sdk/dev-jobs.dockerfile
+++ b/sdk/dev-jobs.dockerfile
@@ -14,12 +14,12 @@
# of the docker build root.)
FROM debian:9
-MAINTAINER Ward Vandewege <ward at curoverse.com>
+MAINTAINER Peter Amstutz <peter.amstutz at curii.com>
ENV DEBIAN_FRONTEND noninteractive
-ARG pythoncmd=python
-ARG pipcmd=pip
+ARG pythoncmd=python3
+ARG pipcmd=pip3
RUN apt-get update -q && apt-get install -qy --no-install-recommends \
git ${pythoncmd}-pip ${pythoncmd}-virtualenv ${pythoncmd}-dev libcurl4-gnutls-dev \
commit 535ff008c43648a7dadeb3f2176abc1540d4ac9b
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Mon Sep 21 14:33:17 2020 -0400
16856: Make spurious msg "Using empty collection" debug log level
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index a45775470..1e64eeb1d 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -236,7 +236,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0,
# empty collection
pdh = collection.portable_data_hash()
assert (pdh == config.EMPTY_BLOCK_LOCATOR), "Empty collection portable_data_hash did not have expected locator, was %s" % pdh
- logger.info("Using empty collection %s", pdh)
+ logger.debug("Using empty collection %s", pdh)
for c in files:
c.keepref = "%s/%s" % (pdh, c.fn)
commit a58c3c3744fe4673cb8eb4a2b84946144bd2271e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Mon Sep 21 14:25:58 2020 -0400
16856: Pass --disable-color, workbench log doesn't do color codes
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 dcbe03a05..4bfe27278 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -192,6 +192,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
action="store_false", default=True,
help=argparse.SUPPRESS)
+ parser.add_argument("--disable-color", dest="enable_color",
+ action="store_false", default=True,
+ help=argparse.SUPPRESS)
+
parser.add_argument("--disable-js-validation",
action="store_true", default=False,
help=argparse.SUPPRESS)
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index fb23c2ccf..9d14ceeab 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -475,6 +475,7 @@ class RunnerContainer(Runner):
"--api=containers",
"--no-log-timestamps",
"--disable-validate",
+ "--disable-color",
"--eval-timeout=%s" % self.arvrunner.eval_timeout,
"--thread-count=%s" % self.arvrunner.thread_count,
"--enable-reuse" if self.enable_reuse else "--disable-reuse",
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