[ARVADOS] updated: 9aff8a3624b463d3fd4d9302c4d41c7558df4a13
Git user
git at public.curoverse.com
Thu Sep 7 17:05:13 EDT 2017
Summary of changes:
apps/workbench/.gitignore | 4 +
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 5 +-
.../app/assets/javascripts/application.js | 9 +-
.../assets/javascripts/components/collections.js | 170 +++++++++++++++++++++
.../app/assets/javascripts/components/date.js | 9 ++
.../assets/javascripts/components/save_ui_state.js | 90 +++++++++++
.../app/assets/javascripts/components/sessions.js | 101 ++++++++++++
.../app/assets/javascripts/components/test.js | 17 +++
.../app/assets/javascripts/mithril_mount.js | 9 ++
.../app/assets/javascripts/models/loader.js | 159 +++++++++++++++++++
.../app/assets/javascripts/models/session_db.js | 130 ++++++++++++++++
.../app/controllers/collections_controller.rb | 2 +-
.../app/controllers/sessions_controller.rb | 13 +-
.../workbench/app/controllers/status_controller.rb | 17 +++
.../human.rb => controllers/tests_controller.rb} | 6 +-
.../workbench/app/views/collections/multisite.html | 5 +
.../jobs/_rerun_job_with_options_popup.html.erb | 15 +-
.../app/views/layouts/application.html.erb | 5 +
apps/workbench/app/views/layouts/body.html.erb | 48 +++---
apps/workbench/app/views/sessions/index.html | 5 +
.../{index.html.erb => logged_out.html.erb} | 0
apps/workbench/app/views/tests/mithril.html | 1 +
apps/workbench/config/application.default.yml | 7 +
apps/workbench/config/application.rb | 5 +
apps/workbench/config/routes.rb | 8 +-
apps/workbench/npm_packages | 11 ++
apps/workbench/test/diagnostics/pipeline_test.rb | 2 +-
apps/workbench/test/integration/search_box_test.rb | 10 +-
apps/workbench/test/integration/smoke_test.rb | 6 +
apps/workbench/test/performance/browsing_test.rb | 2 +-
build/libcloud-pin.sh | 2 +-
build/package-build-dockerfiles/Makefile | 6 +-
build/package-build-dockerfiles/centos7/Dockerfile | 4 +
build/package-build-dockerfiles/debian8/Dockerfile | 4 +
build/package-build-dockerfiles/debian9/Dockerfile | 7 +-
.../ubuntu1204/Dockerfile | 4 +
.../ubuntu1404/Dockerfile | 4 +
.../ubuntu1604/Dockerfile | 4 +
build/run-build-packages.sh | 1 +
build/run-tests.sh | 25 ++-
.../install-nodemanager.html.textile.liquid | 5 +
doc/sdk/python/example.html.textile.liquid | 2 +-
sdk/go/manifest/manifest.go | 4 +-
.../crunch-dispatch-slurm_test.go | 4 +-
services/crunch-run/crunchrun.go | 12 +-
services/crunchstat/crunchstat.go | 2 +-
services/fuse/tests/integration_test.py | 25 ++-
services/fuse/tests/mount_test_base.py | 10 +-
services/fuse/tests/test_exec.py | 7 +-
services/keepstore/s3_volume.go | 34 +++++
services/keepstore/s3_volume_test.go | 6 +-
.../arvnodeman/computenode/driver/ec2.py | 8 +-
.../nodemanager/arvnodeman/test/fake_driver.py | 2 +
services/nodemanager/doc/ec2.example.cfg | 5 +
services/nodemanager/setup.py | 6 +-
.../tests/test_computenode_driver_ec2.py | 21 +--
services/ws/event_source.go | 2 +-
.../arvbox/docker/service/workbench/run-service | 1 +
tools/crunchstat-summary/tests/test_examples.py | 79 ++++++++++
60 files changed, 1064 insertions(+), 105 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/components/collections.js
create mode 100644 apps/workbench/app/assets/javascripts/components/date.js
create mode 100644 apps/workbench/app/assets/javascripts/components/save_ui_state.js
create mode 100644 apps/workbench/app/assets/javascripts/components/sessions.js
create mode 100644 apps/workbench/app/assets/javascripts/components/test.js
create mode 100644 apps/workbench/app/assets/javascripts/mithril_mount.js
create mode 100644 apps/workbench/app/assets/javascripts/models/loader.js
create mode 100644 apps/workbench/app/assets/javascripts/models/session_db.js
create mode 100644 apps/workbench/app/controllers/status_controller.rb
copy apps/workbench/app/{models/human.rb => controllers/tests_controller.rb} (51%)
create mode 100644 apps/workbench/app/views/collections/multisite.html
create mode 100644 apps/workbench/app/views/sessions/index.html
rename apps/workbench/app/views/sessions/{index.html.erb => logged_out.html.erb} (100%)
create mode 100644 apps/workbench/app/views/tests/mithril.html
create mode 100644 apps/workbench/npm_packages
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commit 9aff8a3624b463d3fd4d9302c4d41c7558df4a13
Merge: 80ffee2 23d1b7c
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Thu Sep 7 17:04:58 2017 -0400
10472: Merge branch 'master' into 10472-csummary-cwl-pipeline
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
commit 80ffee29868b8d5ef8faed11e3adf0c3b78c4178
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Thu Sep 7 17:03:04 2017 -0400
10472: Add test for arvados-cwl-runner job tree.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/tools/crunchstat-summary/tests/test_examples.py b/tools/crunchstat-summary/tests/test_examples.py
index ecc8b9d..6271f56 100644
--- a/tools/crunchstat-summary/tests/test_examples.py
+++ b/tools/crunchstat-summary/tests/test_examples.py
@@ -193,3 +193,82 @@ class SummarizePipeline(ReportDiff):
mock.call('fake-log-pdh-2'),
], any_order=True)
mock_cr().open.assert_called_with('fake-logfile.txt')
+
+
+class SummarizeACRJob(ReportDiff):
+ fake_job = {
+ 'uuid': 'zzzzz-8i9sb-i3e77t9z5y8j9cc',
+ 'owner_uuid': 'zzzzz-tpzed-xurymjxw79nv3jz',
+ 'components': {
+ 'foo': 'zzzzz-8i9sb-000000000000000',
+ 'bar': 'zzzzz-8i9sb-000000000000001',
+ 'unfinished-job': 'zzzzz-8i9sb-xxxxxxxxxxxxxxx',
+ 'baz': 'zzzzz-8i9sb-000000000000002',
+ }
+ }
+ fake_jobs_index = { 'items': [
+ {
+ 'uuid': 'zzzzz-8i9sb-000000000000000',
+ 'log': 'fake-log-pdh-0',
+ 'runtime_constraints': {
+ 'min_ram_mb_per_node': 900,
+ 'min_cores_per_node': 1,
+ },
+ },
+ {
+ 'uuid': 'zzzzz-8i9sb-000000000000001',
+ 'log': 'fake-log-pdh-1',
+ 'runtime_constraints': {
+ 'min_ram_mb_per_node': 900,
+ 'min_cores_per_node': 1,
+ },
+ },
+ {
+ 'uuid': 'zzzzz-8i9sb-xxxxxxxxxxxxxxx',
+ },
+ {
+ 'uuid': 'zzzzz-8i9sb-000000000000002',
+ 'log': 'fake-log-pdh-2',
+ 'runtime_constraints': {
+ 'min_ram_mb_per_node': 900,
+ 'min_cores_per_node': 1,
+ },
+ },
+ ]}
+ @mock.patch('arvados.collection.CollectionReader')
+ @mock.patch('arvados.api')
+ def test_acr_job(self, mock_api, mock_cr):
+ logfile = os.path.join(TESTS_DIR, 'logfile_20151204190335.txt.gz')
+ mock_api().jobs().index().execute.return_value = self.fake_jobs_index
+ mock_api().jobs().get().execute.return_value = self.fake_job
+ mock_cr().__iter__.return_value = ['fake-logfile.txt']
+ mock_cr().open.side_effect = [gzip.open(logfile) for _ in range(3)]
+ args = crunchstat_summary.command.ArgumentParser().parse_args(
+ ['--job', self.fake_job['uuid']])
+ cmd = crunchstat_summary.command.Command(args)
+ cmd.run()
+
+ job_report = [
+ line for line in open(logfile+'.report').readlines()
+ if not line.startswith('#!! ')]
+ expect = (
+ ['### Summary for zzzzz-8i9sb-i3e77t9z5y8j9cc (partial) (zzzzz-8i9sb-i3e77t9z5y8j9cc)\n',
+ '(no report generated)\n',
+ '\n'] +
+ ['### Summary for bar (zzzzz-8i9sb-000000000000001)\n'] +
+ job_report + ['\n'] +
+ ['### Summary for baz (zzzzz-8i9sb-000000000000002)\n'] +
+ job_report + ['\n'] +
+ ['### Summary for foo (zzzzz-8i9sb-000000000000000)\n'] +
+ job_report + ['\n'] +
+ ['### Summary for unfinished-job (partial) (zzzzz-8i9sb-xxxxxxxxxxxxxxx)\n',
+ '(no report generated)\n']
+ )
+ self.diff_report(cmd, expect)
+ mock_cr.assert_has_calls(
+ [
+ mock.call('fake-log-pdh-0'),
+ mock.call('fake-log-pdh-1'),
+ mock.call('fake-log-pdh-2'),
+ ], any_order=True)
+ mock_cr().open.assert_called_with('fake-logfile.txt')
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