[ARVADOS] updated: 1.2.0-46-ge4fca76d5

Git user git at public.curoverse.com
Wed Aug 22 06:30:26 EDT 2018


Summary of changes:
 apps/workbench/app/helpers/application_helper.rb   |  14 +-
 .../application/_show_text_with_locators.html.erb  |  49 +-
 .../container_requests_controller_test.rb          |   2 +
 .../test/controllers/projects_controller_test.rb   |  14 +-
 build/build.list                                   |   7 +-
 build/package-build-dockerfiles/Makefile           |   6 +-
 build/package-testing/deb-common-test-packages.sh  |   8 +-
 build/run-library.sh                               |   9 +-
 doc/admin/metrics.html.textile.liquid              |  30 +-
 doc/api/methods/groups.html.textile.liquid         |  21 +
 sdk/cwl/arvados_cwl/arvcontainer.py                |   2 +-
 sdk/cwl/arvados_cwl/fsaccess.py                    |  13 +-
 sdk/cwl/arvados_cwl/runner.py                      |  11 +-
 sdk/cwl/setup.py                                   |   6 +-
 sdk/cwl/tests/13931-size-job.yml                   |   3 +
 sdk/cwl/tests/13931-size.cwl                       |  10 +
 sdk/cwl/tests/13976-keepref-wf.cwl                 |  17 +
 sdk/cwl/tests/arvados-tests.sh                     |   4 +
 sdk/cwl/tests/arvados-tests.yml                    |  17 +
 sdk/cwl/tests/test_container.py                    |   3 +-
 sdk/cwl/tests/test_job.py                          |   4 +-
 sdk/cwl/tests/test_submit.py                       |  10 +-
 sdk/cwl/tests/wf/expect_packed.cwl                 |   3 +-
 sdk/dev-jobs.dockerfile                            |   2 +-
 sdk/go/dispatch/dispatch.go                        |  23 +-
 .../api/app/controllers/application_controller.rb  |   8 +-
 .../controllers/arvados/v1/groups_controller.rb    |  63 ++-
 services/api/app/models/collection.rb              |  20 +-
 services/api/app/models/container_request.rb       |  38 ++
 services/api/config/routes.rb                      |   1 +
 .../migrate/20180806133039_index_all_filenames.rb  |  12 +
 ...30357_add_pdh_and_trash_index_to_collections.rb |   9 +
 ...80820135808_drop_pdh_index_from_collections.rb} |   4 +-
 services/api/db/structure.sql                      | 629 +++++++++++----------
 services/api/lib/load_param.rb                     |  14 +-
 .../test/fixtures/api_client_authorizations.yml    |   7 +
 services/api/test/fixtures/container_requests.yml  |   2 +-
 services/api/test/fixtures/containers.yml          |   2 +-
 services/api/test/fixtures/groups.yml              |   8 +
 .../v1/container_requests_controller_test.rb       |   6 +-
 .../arvados/v1/groups_controller_test.rb           | 131 ++++-
 services/api/test/unit/container_request_test.rb   |  30 +-
 services/api/test/unit/container_test.rb           |   8 +-
 .../crunch-dispatch-local_test.go                  |   2 +-
 .../crunch-dispatch-slurm/crunch-dispatch-slurm.go |  10 +-
 .../crunch-dispatch-slurm_test.go                  |   4 +-
 services/crunch-dispatch-slurm/squeue.go           |  72 ++-
 services/crunch-dispatch-slurm/usage.go            |   1 +
 services/fuse/arvados_fuse/fusedir.py              |  74 ++-
 services/keep-web/cache.go                         |  33 --
 services/keep-web/cache_test.go                    |  87 ++-
 services/keep-web/handler.go                       |  16 +-
 services/keep-web/handler_test.go                  |   2 +-
 services/keep-web/status_test.go                   |   1 -
 54 files changed, 998 insertions(+), 584 deletions(-)
 create mode 100644 sdk/cwl/tests/13931-size-job.yml
 create mode 100644 sdk/cwl/tests/13931-size.cwl
 create mode 100644 sdk/cwl/tests/13976-keepref-wf.cwl
 create mode 100644 services/api/db/migrate/20180806133039_index_all_filenames.rb
 create mode 100644 services/api/db/migrate/20180820130357_add_pdh_and_trash_index_to_collections.rb
 copy services/api/db/migrate/{20130107181109_add_uuid_to_collections.rb => 20180820135808_drop_pdh_index_from_collections.rb} (50%)

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commit e4fca76d5db9bd844530454894d07ddc729b4a9a
Merge: f8f3944e6 3df02aa61
Author: Ward Vandewege <wvandewege at veritasgenetics.com>
Date:   Wed Aug 22 06:29:33 2018 -0400

    Merge branch 'master' into 13823-bionic
    
    refs #13823
    
    Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege at veritasgenetics.com>

diff --cc build/build.list
index b1253c9b6,5196e9c64..f2197ecdb
--- a/build/build.list
+++ b/build/build.list
@@@ -8,31 -8,31 +8,31 @@@ debian8,debian9,ubuntu1404,ubuntu1604,u
  debian8,debian9,ubuntu1404,centos7|oauth2client|1.5.2|2|python|all
  debian8,debian9,ubuntu1404,centos7|pyasn1|0.1.7|2|python|all
  debian8,debian9,ubuntu1404,centos7|pyasn1-modules|0.0.5|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|rsa|3.4.2|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|uritemplate|3.0.0|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|httplib2|0.9.2|3|python|all
 -debian8,debian9,centos7|ws4py|0.3.5|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|rsa|3.4.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|uritemplate|3.0.0|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|httplib2|0.9.2|3|python|all
 +debian8,debian9,centos7|ws4py|0.4.2|2|python|all
  debian8,debian9,centos7|pykka|1.2.1|2|python|all
  debian8,debian9,ubuntu1404,centos7|six|1.10.0|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|ciso8601|1.0.6|3|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|ciso8601|1.0.6|3|python|amd64
  debian8,debian9,centos7|pycrypto|2.6.1|3|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604|backports.ssl_match_hostname|3.5.0.1|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|llfuse|1.2|3|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804|backports.ssl_match_hostname|3.5.0.1|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|llfuse|1.2|3|python|amd64
  debian8,debian9,ubuntu1404,centos7|pycurl|7.19.5.3|3|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|pyyaml|3.12|2|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|rdflib|4.2.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|pyyaml|3.12|2|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|rdflib|4.2.2|2|python|all
  debian8,debian9,ubuntu1404,centos7|shellescape|3.4.1|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|mistune|0.7.3|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|typing|3.6.4|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|avro|1.8.1|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|mistune|0.7.3|2|python|all
- debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|typing|3.5.3.0|2|python|all
++debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|typing|3.6.4|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|avro|1.8.1|2|python|all
  debian8,debian9,ubuntu1404,centos7|ruamel.ordereddict|0.4.9|2|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|cachecontrol|0.11.7|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|pathlib2|2.3.2|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|scandir|1.7|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|docker-py|1.7.2|2|python3|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|cachecontrol|0.11.7|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|pathlib2|2.3.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|scandir|1.7|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|docker-py|1.7.2|2|python3|all
  debian8,debian9,centos7|six|1.10.0|2|python3|all
  debian8,debian9,ubuntu1404,centos7|requests|2.12.4|2|python3|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|websocket-client|0.37.0|2|python3|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|websocket-client|0.37.0|2|python3|all
  ubuntu1404|requests|2.4.3|2|python|all
  centos7|contextlib2|0.5.4|2|python|all
  centos7|isodate|0.5.4|2|python|all
@@@ -40,9 -40,11 +40,11 @@@ centos7|python-daemon|2.1.2|1|python|al
  centos7|pbr|0.11.1|2|python|all
  centos7|pyparsing|2.1.10|2|python|all
  centos7|keepalive|0.5|2|python|all
+ centos7|networkx|1.11|0|python|all
+ centos7|psutil|5.0.1|0|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|lockfile|0.12.2|2|python|all|--epoch 1
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|subprocess32|3.5.1|2|python|all
 -all|ruamel.yaml|0.14.12|2|python|amd64|--python-setup-py-arguments --single-version-externally-managed
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|lockfile|0.12.2|2|python|all|--epoch 1
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|subprocess32|3.5.1|2|python|all
 +centos7,debian8,debian9,ubuntu1404,ubuntu1604|ruamel.yaml|0.15.34|1|python|amd64|--python-setup-py-arguments --single-version-externally-managed
  all|cwltest|1.0.20180518074130|4|python|all|--depends 'python-futures >= 3.0.5' --depends 'python-subprocess32 >= 3.5.0'
  all|junit-xml|1.8|3|python|all
  all|rdflib-jsonld|0.4.0|2|python|all
diff --cc build/package-build-dockerfiles/Makefile
index b7f5aa553,f19f17fc0..9dc536bf1
--- a/build/package-build-dockerfiles/Makefile
+++ b/build/package-build-dockerfiles/Makefile
@@@ -2,7 -2,7 +2,7 @@@
  #
  # SPDX-License-Identifier: AGPL-3.0
  
- all: centos7/generated debian8/generated debian9/generated ubuntu1204/generated ubuntu1404/generated ubuntu1604/generated ubuntu1804/generated
 -all: centos7/generated debian8/generated debian9/generated ubuntu1404/generated ubuntu1604/generated
++all: centos7/generated debian8/generated debian9/generated ubuntu1404/generated ubuntu1604/generated ubuntu1804/generated
  
  centos7/generated: common-generated-all
  	test -d centos7/generated || mkdir centos7/generated
diff --cc sdk/cwl/setup.py
index 1205ba4fd,3b4dfbe99..e452ce264
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@@ -33,10 -33,10 +33,10 @@@ setup(name='arvados-cwl-runner'
        # Note that arvados/build/run-build-packages.sh looks at this
        # file to determine what version of cwltool and schema-salad to build.
        install_requires=[
-           'cwltool==1.0.20180615183820',
-           'schema-salad==2.7.20180501211602',
-           'typing >= 3.5.3',
+           'cwltool==1.0.20180806194258',
+           'schema-salad==2.7.20180719125426',
+           'typing >= 3.6.4',
 -          'ruamel.yaml >=0.13.11, <0.15',
 +          'ruamel.yaml >=0.13.11, <0.16',
            'arvados-python-client>=1.1.4.20180607143841',
            'setuptools',
            'ciso8601 >=1.0.6, <2.0.0',

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