[ARVADOS] updated: 76f9268395068d47fda7f34426bc83d603c834c7
git at public.curoverse.com
git at public.curoverse.com
Thu Mar 13 17:57:34 EDT 2014
Summary of changes:
COPYING | 11 +
LICENSE-2.0.txt | 202 ++++++
README | 21 +
agpl-3.0.txt | 661 +++++++++++++++++++
by-sa-3.0.txt | 297 +++++++++
doc/_config.yml | 10 +-
doc/_layouts/default.html.liquid | 10 +-
doc/install/index.html.md.liquid | 1 +
doc/install/install-api-server.html.md.liquid | 110 ----
doc/install/install-api-server.html.textile.liquid | 128 ++++
doc/install/install-sso.html.textile.liquid | 24 +
doc/install/install-workbench-app.html.md.liquid | 63 --
.../install-workbench-app.html.textile.liquid | 54 ++
doc/user/copying/LICENSE-2.0.html | 182 ++++++
doc/user/copying/agpl-3.0.html | 684 ++++++++++++++++++++
doc/user/copying/by-sa-3.0.html | 418 ++++++++++++
doc/user/copying/copying.html.textile.liquid | 11 +
docker/arvdock | 4 +-
sdk/cli/bin/crunch-job | 41 +-
services/api/Gemfile | 8 +-
services/api/Gemfile.lock | 2 +
.../api/app/controllers/application_controller.rb | 26 +-
.../app/controllers/user_sessions_controller.rb | 3 +-
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 17 +-
services/api/config/application.rb | 26 -
services/api/config/application.yml.example | 20 +-
services/api/config/database.yml.sample | 8 +-
.../api/config/initializers/omniauth.rb.example | 2 +-
29 files changed, 2785 insertions(+), 261 deletions(-)
create mode 100644 COPYING
create mode 100644 LICENSE-2.0.txt
create mode 100644 README
create mode 100644 agpl-3.0.txt
create mode 100644 by-sa-3.0.txt
delete mode 100644 doc/install/install-api-server.html.md.liquid
create mode 100644 doc/install/install-api-server.html.textile.liquid
create mode 100644 doc/install/install-sso.html.textile.liquid
delete mode 100644 doc/install/install-workbench-app.html.md.liquid
create mode 100644 doc/install/install-workbench-app.html.textile.liquid
create mode 100644 doc/user/copying/LICENSE-2.0.html
create mode 100644 doc/user/copying/agpl-3.0.html
create mode 100644 doc/user/copying/by-sa-3.0.html
create mode 100644 doc/user/copying/copying.html.textile.liquid
via 76f9268395068d47fda7f34426bc83d603c834c7 (commit)
via ced5e21f292fd8afa2cf2dc3345eb8a1c714d9cf (commit)
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via 34b27c7729e9d9718d1f99947126252ecdb8be38 (commit)
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commit 76f9268395068d47fda7f34426bc83d603c834c7
Merge: ced5e21 113d3f9
Author: Tim Pierce <twp at curoverse.com>
Date: Thu Mar 13 17:58:57 2014 -0400
Merge branch 'master' into 2221-complete-docker
commit ced5e21f292fd8afa2cf2dc3345eb8a1c714d9cf
Author: Tim Pierce <twp at curoverse.com>
Date: Thu Mar 13 17:57:57 2014 -0400
Save logs to a temp file and commit to Keep via 'arv keep put'. Refs #2221.
diff --git a/docker/arvdock b/docker/arvdock
index ed8da8b..b2fa4b2 100755
--- a/docker/arvdock
+++ b/docker/arvdock
@@ -34,7 +34,7 @@ function start_container {
fi
if [[ "$2" != '' ]]; then
local name="$2"
- args="$args -name $name"
+ args="$args --name $name"
fi
if [[ "$3" != '' ]]; then
local volume="$3"
@@ -42,7 +42,7 @@ function start_container {
fi
if [[ "$4" != '' ]]; then
local link="$4"
- args="$args -link $link"
+ args="$args --link $link"
fi
local image=$5
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 5d362f4..e6fa9fb 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -73,6 +73,7 @@ use Arvados;
use Getopt::Long;
use IPC::Open2;
use IO::Select;
+use File::Temp;
$ENV{"TMPDIR"} ||= "/tmp";
unless (defined $ENV{"CRUNCH_TMP"}) {
@@ -165,11 +166,8 @@ else
}
$job_id = $Job->{'uuid'};
-# $metastream = Warehouse::Stream->new(whc => new Warehouse);
-# $metastream->clear;
-# $metastream->name('.');
-# $metastream->write_start($job_id . '.log.txt');
-
+my $keep_logfile = $job_id . '.log.txt';
+my $local_logfile = File::Temp->new();
$Job->{'runtime_constraints'} ||= {};
$Job->{'runtime_constraints'}->{'max_tasks_per_node'} ||= 0;
@@ -1079,7 +1077,7 @@ sub collate_output
}
if (!defined $joboutput) {
my $s = IO::Select->new($child_out);
- sysread($child_out, $joboutput, 64 * 1024 * 1024) if $s->can_read(0);
+ sysread($child_out, $joboutput, 64 * 1024 * 1024) if $s->can_read(5);
}
$child_in->close;
waitpid($pid, 0);
@@ -1158,8 +1156,9 @@ sub Log # ($jobstep_id, $logmessage)
}
print STDERR ((-t STDERR) ? ($datetime." ".$message) : $message);
- # return if !$metastream;
- # $metastream->write_data ($datetime . " " . $message);
+ if ($metastream) {
+ print $metastream $datetime . " " . $message;
+ }
}
@@ -1187,20 +1186,18 @@ sub cleanup
sub save_meta
{
-# my $justcheckpoint = shift; # false if this will be the last meta saved
-# my $m = $metastream;
-# $m = $m->copy if $justcheckpoint;
-# $m->write_finish;
-# my $whc = Warehouse->new;
-# my $loglocator = $whc->store_block ($m->as_string);
-# $arv->{'collections'}->{'create'}->execute('collection' => {
-# 'uuid' => $loglocator,
-# 'manifest_text' => $m->as_string,
-# });
-# undef $metastream if !$justcheckpoint; # otherwise Log() will try to use it
-# Log (undef, "log manifest is $loglocator");
-# $Job->{'log'} = $loglocator;
-# $Job->update_attributes('log', $loglocator) if $job_has_uuid;
+ my $justcheckpoint = shift; # false if this will be the last meta saved
+ return if $justcheckpoint; # checkpointing is not relevant post-Warehouse.pm
+
+ $local_logfile->flush;
+ my $cmd = "arv keep put --filename $keep_logfile ". $local_logfile->filename;
+ my $loglocator = `$cmd`;
+ die "system $cmd failed: $?" if $?;
+
+ $local_logfile = undef; # the temp file is automatically deleted
+ Log (undef, "log manifest is $loglocator");
+ $Job->{'log'} = $loglocator;
+ $Job->update_attributes('log', $loglocator) if $job_has_uuid;
}
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