[ARVADOS] updated: 5cbcd7b2923a9c4e58189dbaa0b482e357291c57

Git user git at public.curoverse.com
Tue May 31 12:53:35 EDT 2016


Summary of changes:
 apps/workbench/test/integration/jobs_test.rb       |  34 ++---
 backports/python-gflags/fpm-info.sh                |   1 -
 build/package-build-dockerfiles/centos6/Dockerfile |   5 +-
 build/package-build-dockerfiles/debian7/Dockerfile |   3 +-
 build/package-build-dockerfiles/debian8/Dockerfile |   3 +-
 .../ubuntu1204/Dockerfile                          |   3 +-
 .../ubuntu1404/Dockerfile                          |   3 +-
 build/package-test-dockerfiles/centos6/Dockerfile  |   7 +-
 build/run-build-packages-one-target.sh             |   4 +-
 build/run-build-packages.sh                        |  19 +--
 crunch_scripts/cwl-runner                          |  16 ++-
 doc/_includes/_note_python27_sc.liquid             |   2 +-
 sdk/{ruby => cwl}/LICENSE-2.0.txt                  |   0
 sdk/{python => cwl}/MANIFEST.in                    |   0
 sdk/cwl/arvados_cwl/__init__.py                    | 124 ++++++++++++-------
 sdk/cwl/setup.py                                   |   5 +-
 sdk/cwl/tests/test_job.py                          |  11 +-
 sdk/cwl/tests/test_submit.py                       |  12 +-
 sdk/cwl/tests/tool/submit_tool.cwl                 |   1 +
 sdk/cwl/tests/wf/inputs_test.cwl                   |   1 +
 sdk/cwl/tests/wf/submit_wf.cwl                     |   1 +
 sdk/python/arvados/commands/arv_copy.py            | 100 +++++++++++++++
 .../test/fixtures/api_client_authorizations.yml    |  10 +-
 services/api/test/fixtures/links.yml               |  42 ++++++-
 services/api/test/fixtures/users.yml               |  16 +++
 services/crunch-run/crunchrun_test.go              |  33 ++++-
 services/crunch-run/logging_test.go                |  23 ++--
 services/datamanager/collection/collection.go      |  14 +--
 services/keepstore/azure_blob_volume.go            | 137 +++++++++++++++++++--
 services/keepstore/azure_blob_volume_test.go       |  33 ++++-
 services/keepstore/s3_volume.go                    |   4 +-
 services/keepstore/volume_generic_test.go          |  62 +++++++++-
 services/keepstore/volume_unix.go                  |   4 +-
 services/nodemanager/arvnodeman/baseactor.py       |  35 +++++-
 .../arvnodeman/computenode/dispatch/__init__.py    |   2 +-
 services/nodemanager/arvnodeman/config.py          |   3 +-
 services/nodemanager/arvnodeman/daemon.py          |   7 +-
 services/nodemanager/arvnodeman/launcher.py        |   7 ++
 services/nodemanager/tests/test_failure.py         |  34 +++--
 tools/arvbox/lib/arvbox/docker/Dockerfile.base     |   9 +-
 40 files changed, 674 insertions(+), 156 deletions(-)
 delete mode 100644 backports/python-gflags/fpm-info.sh
 copy sdk/{ruby => cwl}/LICENSE-2.0.txt (100%)
 copy sdk/{python => cwl}/MANIFEST.in (100%)

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commit 5cbcd7b2923a9c4e58189dbaa0b482e357291c57
Author: radhika <radhika at curoverse.com>
Date:   Tue May 31 12:52:35 2016 -0400

    8876: improve jobs_with_components test to have components that can be un/read

diff --git a/apps/workbench/test/integration/jobs_test.rb b/apps/workbench/test/integration/jobs_test.rb
index 1ad3296..be6a83d 100644
--- a/apps/workbench/test/integration/jobs_test.rb
+++ b/apps/workbench/test/integration/jobs_test.rb
@@ -129,7 +129,7 @@ class JobsTest < ActionDispatch::IntegrationTest
 
   [
     ['active', true],
-    ['job_reader', false],
+    ['job_reader2', false],
   ].each do |user, readable|
     test "view job with components as #{user} user" do
       job = api_fixture('jobs')['running_job_with_components']
@@ -142,26 +142,28 @@ class JobsTest < ActionDispatch::IntegrationTest
       assert page.has_text? job['script_version']
       assert page.has_no_text? 'script_parameters'
 
+      # The job_reader2 is allowed to read job, component2, and component2_child1,
+      # and component2_child2 only as a component of the pipeline component2
       if readable
         assert page.has_link? 'component1'
         assert page.has_link? 'component2'
       else
-        # children are not readable by user
         assert page.has_no_link? 'component1'
-        assert page.has_no_link? 'component2'
-        return
+        assert page.has_link? 'component2'
       end
 
-      click_link('component1')
-      within('#collapse1') do
-        assert(has_text? component1['uuid'])
-        assert(has_text? component1['script_version'])
-        assert(has_text? 'script_parameters')
+      if readable
+        click_link('component1')
+        within('#collapse1') do
+          assert(has_text? component1['uuid'])
+          assert(has_text? component1['script_version'])
+          assert(has_text? 'script_parameters')
+        end
+        click_link('component1')
       end
-      click_link('component1')
 
       click_link('component2')
-      within('#collapse2') do
+      within('.panel-collapse') do
         assert(has_text? component2['uuid'])
         assert(has_text? component2['script_version'])
         assert(has_no_text? 'script_parameters')
@@ -169,16 +171,20 @@ class JobsTest < ActionDispatch::IntegrationTest
         assert(has_link? 'running')
 
         click_link('previous')
-        within('#collapse3') do
+        within('.panel-collapse') do
           assert(has_text? component2_child1['uuid'])
           assert(has_text? component2_child1['script_version'])
         end
         click_link('previous')
 
         click_link('running')
-        within('#collapse4') do
+        within('.panel-collapse') do
           assert(has_text? component2_child2['uuid'])
-          assert(has_text? component2_child2['script_version'])
+          if readable
+            assert(has_text? component2_child2['script_version'])
+          else
+            assert(has_no_text? component2_child2['script_version'])
+          end
         end
       end
     end
diff --git a/services/api/test/fixtures/api_client_authorizations.yml b/services/api/test/fixtures/api_client_authorizations.yml
index d6c0e40..1f9fe07 100644
--- a/services/api/test/fixtures/api_client_authorizations.yml
+++ b/services/api/test/fixtures/api_client_authorizations.yml
@@ -222,6 +222,14 @@ job_reader:
   api_token: e99512cdc0f3415c2428b9758f33bdfb07bc3561b00e86e7e6
   expires_at: 2038-01-01 00:00:00
 
+job_reader2:
+  uuid: zzzzz-gj3su-jobreader2autht
+  api_client: untrusted
+  user: job_reader2
+  api_token: e99512cdc0f3415c2428b9758f33bdfb07bc3561b00e86e7e6
+  api_token: jobreader2415c2428b9758f33bdfb07bc3561b0jobreader2
+  expires_at: 2038-01-01 00:00:00
+
 active_no_prefs:
   uuid: zzzzz-gj3su-307z32aux8dg2s1
   api_client: untrusted
@@ -276,4 +284,4 @@ dispatch1:
   api_client: untrusted
   user: system_user
   api_token: kwi8oowusvbutahacwk2geulqewy5oaqmpalczfna4b6bb0hfw
-  expires_at: 2038-01-01 00:00:00
\ No newline at end of file
+  expires_at: 2038-01-01 00:00:00
diff --git a/services/api/test/fixtures/links.yml b/services/api/test/fixtures/links.yml
index 96e82cc..2d1e552 100644
--- a/services/api/test/fixtures/links.yml
+++ b/services/api/test/fixtures/links.yml
@@ -702,8 +702,8 @@ job_reader_can_read_previous_job_run:
   tail_uuid: zzzzz-tpzed-905b42d1dd4a354
   head_uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
 
-job_reader_can_read_job_with_components:
-  # Permission link giving job_reader permission
+job_reader2_can_read_job_with_components:
+  # Permission link giving job_reader2 permission
   # to read running_job_with_components
   uuid: zzzzz-o0j2j-jobcomps4jobrdr
   owner_uuid: zzzzz-tpzed-000000000000000
@@ -714,11 +714,41 @@ job_reader_can_read_job_with_components:
   updated_at: 2014-06-13 20:42:26 -0800
   link_class: permission
   name: can_read
-  tail_uuid: zzzzz-tpzed-905b42d1dd4a354
+  tail_uuid: zzzzz-tpzed-readjobwithcomp
   head_uuid: zzzzz-8i9sb-with2components
 
-job_reader_can_read_foo_repo:
-  # Permission link giving job_reader permission
+job_reader2_can_read_pipeline_from_job_with_components:
+  # Permission link giving job_reader2 permission
+  # to read running_job_with_components
+  uuid: zzzzz-o0j2j-pi4comps4jobrdr
+  owner_uuid: zzzzz-tpzed-000000000000000
+  created_at: 2014-06-13 20:42:26 -0800
+  modified_by_client_uuid: zzzzz-tpzed-000000000000000
+  modified_by_user_uuid: zzzzz-tpzed-000000000000000
+  modified_at: 2014-06-13 20:42:26 -0800
+  updated_at: 2014-06-13 20:42:26 -0800
+  link_class: permission
+  name: can_read
+  tail_uuid: zzzzz-tpzed-readjobwithcomp
+  head_uuid: zzzzz-d1hrv-partdonepipelin
+
+job_reader2_can_read_first_job_from_pipeline_from_job_with_components:
+  # Permission link giving job_reader2 permission
+  # to read running_job_with_components
+  uuid: zzzzz-o0j2j-job4pi4j4jobrdr
+  owner_uuid: zzzzz-tpzed-000000000000000
+  created_at: 2014-06-13 20:42:26 -0800
+  modified_by_client_uuid: zzzzz-tpzed-000000000000000
+  modified_by_user_uuid: zzzzz-tpzed-000000000000000
+  modified_at: 2014-06-13 20:42:26 -0800
+  updated_at: 2014-06-13 20:42:26 -0800
+  link_class: permission
+  name: can_read
+  tail_uuid: zzzzz-tpzed-readjobwithcomp
+  head_uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
+
+job_reader2_can_read_foo_repo:
+  # Permission link giving job_reader2 permission
   # to read foo_repo
   uuid: zzzzz-o0j2j-072ec05dc9487f8
   owner_uuid: zzzzz-tpzed-000000000000000
@@ -729,7 +759,7 @@ job_reader_can_read_foo_repo:
   updated_at: 2014-06-13 20:42:26 -0800
   link_class: permission
   name: can_read
-  tail_uuid: zzzzz-tpzed-905b42d1dd4a354
+  tail_uuid: zzzzz-tpzed-readjobwithcomp
   head_uuid: zzzzz-s0uqq-382brsig8rp3666
 
 baz_collection_name_in_asubproject:
diff --git a/services/api/test/fixtures/users.yml b/services/api/test/fixtures/users.yml
index b15ada1..7104af2 100644
--- a/services/api/test/fixtures/users.yml
+++ b/services/api/test/fixtures/users.yml
@@ -209,6 +209,22 @@ job_reader:
       role: Computational biologist
     getting_started_shown: 2015-03-26 12:34:56.789000000 Z
 
+job_reader2:
+  owner_uuid: zzzzz-tpzed-000000000000000
+  uuid: zzzzz-tpzed-readjobwithcomp
+  email: job_reader2 at arvados.local
+  first_name: Job
+  last_name: Reader2
+  identity_url: https://job_reader2.openid.local
+  is_active: true
+  is_admin: false
+  username: jobreader2
+  prefs:
+    profile:
+      organization: example.com
+      role: Computational biologist
+    getting_started_shown: 2015-03-26 12:34:56.789000000 Z
+
 active_no_prefs:
   owner_uuid: zzzzz-tpzed-000000000000000
   uuid: zzzzz-tpzed-a46c42d1td4aoj4

commit a31816b03c8249178d51621524f05437f5f9478a
Merge: a0187bc 63e7b75
Author: radhika <radhika at curoverse.com>
Date:   Tue May 31 11:42:42 2016 -0400

    Merge branch 'master' into 8876-work-unit


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