[ARVADOS] updated: 88d55c312b6ec1e3b849cc26d814d4f642c1ff7d
git at public.curoverse.com
git at public.curoverse.com
Tue Mar 4 19:59:31 EST 2014
Summary of changes:
apps/admin/setup-new-user.rb | 6 +-
.../app/assets/javascripts/application.js | 55 ++++
.../app/assets/stylesheets/application.css.scss | 20 ++-
apps/workbench/app/assets/stylesheets/loading.css | 29 +-
.../app/controllers/application_controller.rb | 4 +-
.../app/controllers/collections_controller.rb | 4 +-
.../app/views/collections/_index_tbody.html.erb | 21 +-
.../app/views/collections/_show_files.html.erb | 2 +-
.../app/views/collections/_show_recent.html.erb | 6 +-
.../app/views/layouts/application.html.erb | 2 +-
.../app/views/pipeline_instances/show.html.erb | 1 +
.../{_show_graph.js.erb => show.js.erb} | 3 +-
crunch_scripts/hash | 24 +-
doc/Rakefile | 2 +-
doc/_config.yml | 9 +-
doc/_includes/_navbar_top.liquid | 10 +-
doc/install/install-api-server.html.md.liquid | 12 +-
.../install-crunch-dispatch.html.textile.liquid | 16 +-
doc/sdk/python/sdk-python.html.textile.liquid | 6 +-
.../check-environment.html.textile.liquid | 6 +-
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/reference/sdk-cli.html.textile.liquid | 6 +-
.../running-external-program.html.textile.liquid | 6 +-
.../tutorial-firstscript.html.textile.liquid | 2 +-
...rial-gatk-variantfiltration.html.textile.liquid | 4 +-
.../tutorial-job-debug.html.textile.liquid | 2 +-
.../tutorials/tutorial-job1.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 2 +-
.../tutorial-new-pipeline.html.textile.liquid | 4 +-
.../tutorial-parallel.html.textile.liquid | 6 +-
.../tutorial-trait-search.html.textile.liquid | 2 +-
docker/README.md | 39 +--
docker/api/passenger.conf | 6 +-
docker/base/Dockerfile | 8 +-
docker/sso/passenger.conf | 6 +-
docker/workbench/passenger.conf | 6 +-
sdk/cli/bin/arv | 4 +-
sdk/cli/bin/arv-ls | 1 +
sdk/cli/bin/arv-mount | 1 +
sdk/cli/bin/arv-normalize | 1 +
sdk/cli/bin/crunch-job | 25 +-
sdk/python/arvados/__init__.py | 13 +-
sdk/python/arvados/collection.py | 90 +++++-
sdk/python/arvados/fuse.py | 317 +++++++++++++++++++
sdk/python/arvados/keep.py | 140 +++++++--
sdk/python/arvados/stream.py | 326 +++++++++++--------
sdk/python/arvados/timer.py | 16 +
sdk/python/bin/arv-ls | 33 ++
sdk/python/bin/arv-mount | 195 +++---------
sdk/python/bin/arv-normalize | 24 ++
sdk/python/bin/arv-put | 16 +
sdk/python/readme.llfuse | 1 +
sdk/python/requirements.txt | 2 +-
sdk/python/setup.py.src | 3 +-
sdk/python/test_collections.py | 334 ++++++++++++++++++--
sdk/python/test_mount.py | 153 +++++++++
sdk/python/testdata/1000G_ref_manifest | 1 +
sdk/python/testdata/jlake_manifest | 20 ++
sdk/ruby/Gemfile.lock | 8 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 1 +
services/api/app/models/collection.rb | 27 ++-
services/api/app/models/node.rb | 28 +-
services/api/script/crunch-dispatch.rb | 26 ++-
.../arvados/v1/collections_controller_test.rb | 39 ++-
.../api/test/integration/collections_api_test.rb | 4 -
services/api/test/integration/jobs_api_test.rb | 23 ++
services/api/test/test_helper.rb | 6 +
67 files changed, 1700 insertions(+), 519 deletions(-)
create mode 120000 apps/workbench/app/views/pipeline_instances/show.html.erb
rename apps/workbench/app/views/pipeline_instances/{_show_graph.js.erb => show.js.erb} (74%)
create mode 120000 sdk/cli/bin/arv-ls
create mode 120000 sdk/cli/bin/arv-mount
create mode 120000 sdk/cli/bin/arv-normalize
create mode 100644 sdk/python/arvados/fuse.py
create mode 100644 sdk/python/arvados/timer.py
create mode 100755 sdk/python/bin/arv-ls
create mode 100755 sdk/python/bin/arv-normalize
create mode 100644 sdk/python/readme.llfuse
create mode 100644 sdk/python/test_mount.py
create mode 100644 sdk/python/testdata/1000G_ref_manifest
create mode 100644 sdk/python/testdata/jlake_manifest
create mode 100644 services/api/test/integration/jobs_api_test.rb
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commit 88d55c312b6ec1e3b849cc26d814d4f642c1ff7d
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Mar 4 19:59:22 2014 -0500
Set up virtualenv even if no arvados/sdk/python present. refs #2199 refs #2197
diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 2ba36f2..392bd7e 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -332,10 +332,10 @@ my $skip_install = ($local_job && $Job->{script_version} =~ m{^/});
if ($skip_install)
{
$ENV{"CRUNCH_SRC"} = $Job->{script_version};
+ system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0
+ or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8));
for my $src_path ("$ENV{CRUNCH_SRC}/arvados/sdk/python") {
if (-d $src_path) {
- system("virtualenv", "$ENV{CRUNCH_TMP}/opt") == 0
- or croak ("virtualenv $ENV{CRUNCH_TMP}/opt failed: exit ".($?>>8));
system ("cd $src_path && ./build.sh && \$CRUNCH_TMP/opt/bin/python setup.py install")
== 0
or croak ("setup.py in $src_path failed: exit ".($?>>8));
@@ -1386,9 +1386,9 @@ chomp ($pwd = `pwd`);
my $install_dir = $ENV{"CRUNCH_INSTALL"} || "$pwd/opt";
mkdir $install_dir;
+shell_or_die ("virtualenv", $install_dir);
for my $src_path ("$destdir/arvados/sdk/python") {
if (-d $src_path) {
- shell_or_die ("virtualenv", $install_dir);
shell_or_die ("cd $src_path && ./build.sh && $install_dir/bin/python setup.py install");
}
}
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