[ARVADOS] updated: 3678eda6ea138d948919944d1b54e680ba20ea81
Git user
git at public.curoverse.com
Tue Aug 30 15:38:40 EDT 2016
Summary of changes:
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 2 +
.../app/controllers/collections_controller.rb | 7 -
.../controllers/container_requests_controller.rb | 45 ++-
.../controllers/work_unit_templates_controller.rb | 30 ++
.../app/controllers/work_units_controller.rb | 77 ++++
apps/workbench/app/helpers/application_helper.rb | 143 +++++++
apps/workbench/app/models/container_work_unit.rb | 7 +
.../app/models/pipeline_instance_work_unit.rb | 4 +
apps/workbench/app/models/work_unit.rb | 4 +
.../_choose_rows.html.erb | 0
apps/workbench/app/views/collections/show.html.erb | 40 +-
.../views/container_requests/_show_inputs.html.erb | 40 ++
.../app/views/projects/_show_dashboard.html.erb | 8 +-
apps/workbench/app/views/projects/show.html.erb | 10 +-
.../views/workflows/_show_chooser_preview.html.erb | 3 +
apps/workbench/config/load_config.rb | 2 +-
apps/workbench/config/routes.rb | 2 +
.../controllers/collections_controller_test.rb | 7 -
.../test/integration/application_layout_test.rb | 25 ++
.../test/integration/container_requests_test.rb | 99 +++++
apps/workbench/test/integration/projects_test.rb | 23 ++
.../collections_perf_test.rb | 4 +-
build/go-package-scripts/postinst | 31 ++
build/go-package-scripts/prerm | 19 +
build/run-build-docker-images.sh | 8 +-
build/run-library.sh | 13 +-
doc/_config.yml | 6 +
doc/_includes/_install_compute_docker.liquid | 45 +++
doc/_includes/_install_compute_fuse.liquid | 17 +
doc/_includes/_install_docker_cleaner.liquid | 41 ++
.../install-compute-node.html.textile.liquid | 39 ++
.../install-dispatch.html.textile.liquid | 114 ++++++
.../install-prerequisites.html.textile.liquid | 9 +
.../crunch2-slurm/install-test.html.textile.liquid | 109 ++++++
.../install-compute-node.html.textile.liquid | 82 +---
sdk/cwl/tests/test_submit.py | 10 +-
sdk/python/arvados/arvfile.py | 13 +-
sdk/python/arvados/collection.py | 36 +-
sdk/python/tests/test_arvfile.py | 31 +-
sdk/python/tests/test_collections.py | 42 +++
services/api/Gemfile.lock | 3 -
.../app/controllers/arvados/v1/jobs_controller.rb | 153 ++++----
.../api/app/models/api_client_authorization.rb | 4 +-
services/api/app/models/arvados_model.rb | 8 +-
services/api/app/models/collection.rb | 6 -
services/api/app/models/container_request.rb | 4 +-
services/api/app/models/job.rb | 20 +
services/api/config/application.default.yml | 8 +
...9195557_add_script_parameters_digest_to_jobs.rb | 6 +
...0819195725_populate_script_parameters_digest.rb | 21 ++
services/api/db/structure.sql | 16 +-
services/api/test/fixtures/container_requests.yml | 416 +++++++++++++++++++++
services/api/test/fixtures/jobs.yml | 28 ++
services/api/test/fixtures/workflows.yml | 33 +-
.../arvados/v1/job_reuse_controller_test.rb | 4 +-
services/api/test/unit/container_request_test.rb | 6 +-
services/api/test/unit/job_test.rb | 16 +
services/api/test/unit/log_test.rb | 37 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 7 +-
.../crunch-dispatch-slurm.service | 12 +
61 files changed, 1788 insertions(+), 269 deletions(-)
create mode 100644 apps/workbench/app/controllers/work_unit_templates_controller.rb
copy apps/workbench/app/views/{pipeline_templates => application}/_choose_rows.html.erb (100%)
create mode 100644 apps/workbench/app/views/container_requests/_show_inputs.html.erb
create mode 100644 apps/workbench/app/views/workflows/_show_chooser_preview.html.erb
create mode 100644 apps/workbench/test/integration/container_requests_test.rb
create mode 100755 build/go-package-scripts/postinst
create mode 100755 build/go-package-scripts/prerm
create mode 100644 doc/_includes/_install_compute_docker.liquid
create mode 100644 doc/_includes/_install_compute_fuse.liquid
create mode 100644 doc/_includes/_install_docker_cleaner.liquid
create mode 100644 doc/install/crunch2-slurm/install-compute-node.html.textile.liquid
create mode 100644 doc/install/crunch2-slurm/install-dispatch.html.textile.liquid
create mode 100644 doc/install/crunch2-slurm/install-prerequisites.html.textile.liquid
create mode 100644 doc/install/crunch2-slurm/install-test.html.textile.liquid
create mode 100644 services/api/db/migrate/20160819195557_add_script_parameters_digest_to_jobs.rb
create mode 100644 services/api/db/migrate/20160819195725_populate_script_parameters_digest.rb
create mode 100644 services/crunch-dispatch-slurm/crunch-dispatch-slurm.service
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commit 3678eda6ea138d948919944d1b54e680ba20ea81
Merge: a3b87ee 7497b21
Author: Lucas Di Pentima <lucas at curoverse.com>
Date: Tue Aug 30 16:37:48 2016 -0300
Merge branch 'master' into 9687-container-request-display
diff --cc services/api/test/fixtures/container_requests.yml
index e9b3fd4,2216524..433aff2
--- a/services/api/test/fixtures/container_requests.yml
+++ b/services/api/test/fixtures/container_requests.yml
@@@ -151,25 -151,422 +151,441 @@@ running_anonymous_accessible
vcpus: 1
ram: 123
+cr_for_failed:
+ uuid: zzzzz-xvhdp-cr4failedcontnr
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: cr for container exit code not 0
+ state: Committed
+ priority: 1
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ container_image: test
+ cwd: test
+ output_path: test
+ command: ["echo", "hello"]
+ container_uuid: zzzzz-dz642-failedcntnr
+ runtime_constraints:
+ vcpus: 1
+ ram: 123
+
+ uncommitted:
+ uuid: zzzzz-xvhdp-cr4uncommittedc
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: uncommitted
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ command: ["arvados-cwl-runner", "--local", "--api=containers",
+ "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"]
+ output_path: "/var/spool/cwl"
+ cwd: "/var/spool/cwl"
+ priority: 1
+ state: "Uncommitted"
+ container_image: arvados/jobs
+ mounts: {
+ "/var/lib/cwl/workflow.json": {
+ "kind": "json",
+ "content": {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+ "baseCommand": ["echo"],
+ "inputs": [
+ {
+ "doc": "a longer documentation string for this parameter (optional)",
+ "type": "boolean",
+ "id": "ex_boolean",
+ "label": "a short label for this parameter (optional)",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "boolean"],
+ "id": "ex_boolean_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "doc": "directory selection should present the workbench collection picker",
+ "type": "Directory",
+ "id": "ex_dir",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "double",
+ "id": "ex_double",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "doc": "file selection should present the workbench file picker",
+ "type": "File",
+ "id": "ex_file",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "float",
+ "id": "ex_float",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "int",
+ "id": "ex_int",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "int"],
+ "id": "ex_int_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "long",
+ "id": "ex_long",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "string",
+ "id": "ex_string",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "string"],
+ "id": "ex_string_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": {
+ "type": "enum",
+ "symbols": ["a", "b", "c"]
+ },
+ "id": "ex_enum",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", {
+ "type": "enum",
+ "symbols": ["a", "b", "c"]
+ }],
+ "id": "ex_enum_opt",
+ "inputBinding": {"position": 1}
+ }
+ ],
+ "outputs": []
+ }
+ },
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": {}
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": true
+ }
+ }
+ runtime_constraints:
+ vcpus: 1
+ ram: 256000000
+ API: true
+
+ uncommitted_ready_to_run:
+ uuid: zzzzz-xvhdp-cr4uncommittedd
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: uncommitted_ready_to_run
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ command: ["arvados-cwl-runner", "--local", "--api=containers",
+ "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"]
+ output_path: "/var/spool/cwl"
+ cwd: "/var/spool/cwl"
+ priority: 1
+ state: "Uncommitted"
+ container_image: arvados/jobs
+ mounts: {
+ "/var/lib/cwl/workflow.json": {
+ "kind": "json",
+ "content": {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+ "baseCommand": ["echo"],
+ "inputs": [
+ {
+ "doc": "a longer documentation string for this parameter (optional)",
+ "type": "boolean",
+ "id": "ex_boolean",
+ "label": "a short label for this parameter (optional)",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "boolean"],
+ "id": "ex_boolean_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "doc": "directory selection should present the workbench collection picker",
+ "type": "Directory",
+ "id": "ex_dir",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "double",
+ "id": "ex_double",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "doc": "file selection should present the workbench file picker",
+ "type": "File",
+ "id": "ex_file",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "float",
+ "id": "ex_float",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "int",
+ "id": "ex_int",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "int"],
+ "id": "ex_int_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "long",
+ "id": "ex_long",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": "string",
+ "id": "ex_string",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "string"],
+ "id": "ex_string_opt",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": {
+ "type": "enum",
+ "symbols": ["a", "b", "c"]
+ },
+ "id": "ex_enum",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", {
+ "type": "enum",
+ "symbols": ["a", "b", "c"]
+ }],
+ "id": "ex_enum_opt",
+ "inputBinding": {"position": 1}
+ }
+ ],
+ "outputs": []
+ }
+ },
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": {
+ "ex_string_opt": null,
+ "ex_int_opt": null,
+ "ex_boolean": false,
+ "ex_boolean_opt": true,
+ "ex_dir": {
+ "class": "Directory",
+ "location": "keep:1f4b0bc7583c2a7f9102c395f4ffc5e3+45",
+ "arv:collection": "zzzzz-4zz18-znfnqtbbv4spc3w"
+ },
+ "ex_double": 66.0,
+ "ex_file": {
+ "class": "File",
+ "location": "keep:1f4b0bc7583c2a7f9102c395f4ffc5e3+45/foo",
+ "arv:collection": "zzzzz-4zz18-znfnqtbbv4spc3w/foo"
+ },
+ "ex_float": 55.0,
+ "ex_int": 55,
+ "ex_long": 22,
+ "ex_string": "qq",
+ "ex_enum": "a"
+ }
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": true
+ }
+ }
+ runtime_constraints:
+ vcpus: 1
+ ram: 256000000
+ API: true
+
+ uncommitted-with-directory-input:
+ uuid: zzzzz-xvhdp-cr4uncommitted2
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: uncommitted with directory input
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ command: ["arvados-cwl-runner", "--local", "--api=containers",
+ "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"]
+ output_path: "/var/spool/cwl"
+ cwd: "/var/spool/cwl"
+ priority: 1
+ state: Uncommitted
+ container_image: fa3c1a9cb6783f85f2ecda037e07b8c3+167
+ mounts: {
+ "/var/lib/cwl/workflow.json": {
+ "kind": "json",
+ "content": {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+ "baseCommand": ["echo"],
+ "inputs": [
+ {
+ "type": "Directory",
+ "id": "directory_type",
+ "inputBinding": {"position": 1}
+ }
+ ],
+ "outputs": []
+ }
+ },
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": {}
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": true
+ }
+ }
+ runtime_constraints:
+ vcpus: 1
+ ram: 256000000
+ API: true
+
+ uncommitted-with-file-input:
+ uuid: zzzzz-xvhdp-cr4uncommittedf
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: uncommitted with directory input
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ command: ["arvados-cwl-runner", "--local", "--api=containers",
+ "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"]
+ output_path: "/var/spool/cwl"
+ cwd: "/var/spool/cwl"
+ priority: 1
+ state: Uncommitted
+ container_image: fa3c1a9cb6783f85f2ecda037e07b8c3+167
+ mounts: {
+ "/var/lib/cwl/workflow.json": {
+ "kind": "json",
+ "content": {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+ "baseCommand": ["echo"],
+ "inputs": [
+ {
+ "type": "File",
+ "id": "file_type",
+ "inputBinding": {"position": 1}
+ }
+ ],
+ "outputs": []
+ }
+ },
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": {}
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": true
+ }
+ }
+ runtime_constraints:
+ vcpus: 1
+ ram: 256000000
+ API: true
+
+ uncommitted-with-required-and-optional-inputs:
+ uuid: zzzzz-xvhdp-cr4uncommitted3
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: uncommitted with required and optional inputs
+ created_at: 2016-01-11 11:11:11.111111111 Z
+ updated_at: 2016-01-11 11:11:11.111111111 Z
+ modified_at: 2016-01-11 11:11:11.111111111 Z
+ modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ command: ["arvados-cwl-runner", "--local", "--api=containers",
+ "/var/lib/cwl/workflow.json", "/var/lib/cwl/cwl.input.json"]
+ output_path: "/var/spool/cwl"
+ cwd: "/var/spool/cwl"
+ priority: 1
+ state: Uncommitted
+ container_image: fa3c1a9cb6783f85f2ecda037e07b8c3+167
+ mounts: {
+ "/var/lib/cwl/workflow.json": {
+ "kind": "json",
+ "content": {
+ "cwlVersion": "v1.0",
+ "class": "CommandLineTool",
+ "baseCommand": ["echo"],
+ "inputs": [
+ {
+ "type": "int",
+ "id": "int_required",
+ "inputBinding": {"position": 1}
+ },
+ {
+ "type": ["null", "int"],
+ "id": "int_optional",
+ "inputBinding": {"position": 1}
+ }
+ ],
+ "outputs": []
+ }
+ },
+ "/var/lib/cwl/cwl.input.json": {
+ "kind": "json",
+ "content": {}
+ },
+ "stdout": {
+ "kind": "file",
+ "path": "/var/spool/cwl/cwl.output.json"
+ },
+ "/var/spool/cwl": {
+ "kind": "collection",
+ "writable": true
+ }
+ }
+ runtime_constraints:
+ vcpus: 1
+ ram: 256000000
+ API: true
+
# Test Helper trims the rest of the file
# Do not add your fixtures below this line as the rest of this file will be trimmed by test_helper
-----------------------------------------------------------------------
hooks/post-receive
--
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