[ARVADOS] updated: 1.1.4-585-g436971482
Git user
git at public.curoverse.com
Wed Jul 11 09:28:22 EDT 2018
Summary of changes:
.../app/controllers/work_units_controller.rb | 29 ++-
apps/workbench/app/helpers/application_helper.rb | 13 +-
apps/workbench/app/helpers/version_helper.rb | 6 +
.../views/application/_report_issue_popup.html.erb | 6 +-
apps/workbench/config/application.default.yml | 6 +
apps/workbench/lib/app_version.rb | 15 ++
build/build.list | 1 +
build/run-tests.sh | 6 +
doc/_config.yml | 4 +
.../_container_scheduling_parameters.liquid | 2 +
doc/admin/activation.html.textile.liquid | 229 ++++++++++++++++++++
doc/admin/spot-instances.html.textile.liquid | 78 +++++++
doc/api/methods/groups.html.textile.liquid | 2 +-
doc/api/tokens.html.textile.liquid | 4 +
.../arvados-on-kubernetes-GKE.html.textile.liquid | 62 ++++++
...ados-on-kubernetes-minikube.html.textile.liquid | 34 +++
.../arvados-on-kubernetes.html.textile.liquid | 133 ++++++++++++
doc/install/index.html.textile.liquid | 20 +-
doc/user/cwl/cwl-extensions.html.textile.liquid | 23 ++
lib/cmd/cmd.go | 16 +-
lib/controller/handler.go | 6 +
lib/controller/handler_test.go | 8 +
lib/dispatchcloud/node_size.go | 34 +--
lib/dispatchcloud/node_size_test.go | 62 +++---
sdk/R/R/zzz.R | 10 +
sdk/R/README.Rmd | 2 +
sdk/cwl/arvados_cwl/__init__.py | 231 +++++++++++----------
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 44 ++++
sdk/cwl/arvados_cwl/arvcontainer.py | 80 ++++---
sdk/cwl/arvados_cwl/arvjob.py | 54 +++--
sdk/cwl/arvados_cwl/arvtool.py | 73 +++----
sdk/cwl/arvados_cwl/arvworkflow.py | 69 +++---
sdk/cwl/arvados_cwl/context.py | 33 +++
sdk/cwl/arvados_cwl/crunch_script.py | 19 +-
sdk/cwl/arvados_cwl/done.py | 10 +-
sdk/cwl/arvados_cwl/pathmapper.py | 27 ++-
sdk/cwl/arvados_cwl/runner.py | 31 ++-
sdk/cwl/arvados_cwl/util.py | 31 +++
sdk/cwl/arvados_version.py | 17 +-
sdk/cwl/setup.py | 10 +-
.../collection_per_tool_packed.cwl | 126 +++++++----
sdk/cwl/tests/makes_intermediates/echo.cwl | 14 ++
.../cwl/tests/makes_intermediates/hello1.txt | 0
.../tests/makes_intermediates/run_in_single.cwl | 38 ++++
sdk/cwl/tests/makes_intermediates/subwf.cwl | 15 ++
sdk/cwl/tests/test_container.py | 179 ++++++++++------
sdk/cwl/tests/test_job.py | 143 ++++++++-----
sdk/cwl/tests/test_submit.py | 44 +++-
sdk/cwl/tests/test_util.py | 45 ++++
sdk/cwl/tests/wf/expect_packed.cwl | 128 ++++++++----
...ubmit_wf.cwl => submit_wf_runner_resources.cwl} | 6 +
sdk/go/arvados/byte_size.go | 91 ++++++++
sdk/go/arvados/byte_size_test.go | 70 +++++++
sdk/go/arvados/config.go | 50 ++++-
sdk/go/arvados/config_test.go | 37 ++++
sdk/go/arvados/container.go | 3 +-
sdk/python/arvados/__init__.py | 2 -
sdk/python/arvados/api.py | 9 +-
sdk/python/arvados/commands/keepdocker.py | 2 +-
sdk/python/arvados/keep.py | 19 +-
sdk/python/arvados/safeapi.py | 6 +
sdk/python/setup.py | 1 +
sdk/python/tests/test_keep_client.py | 25 +++
.../controllers/arvados/v1/schema_controller.rb | 2 +
.../api/app/models/api_client_authorization.rb | 3 +-
services/api/app/models/container_request.rb | 35 +++-
services/api/app/models/user.rb | 3 +-
services/api/config/application.default.yml | 27 ++-
services/api/lib/app_version.rb | 15 ++
services/api/lib/crunch_dispatch.rb | 8 +-
services/api/lib/update_priority.rb | 25 ++-
services/api/lib/whitelist_update.rb | 2 +-
.../arvados/v1/schema_controller_test.rb | 14 +-
services/api/test/integration/remote_user_test.rb | 33 +++
services/api/test/unit/container_request_test.rb | 49 +++--
services/api/test/unit/update_priority_test.rb | 30 +++
services/api/test/unit/user_test.rb | 4 +-
.../crunch-dispatch-slurm_test.go | 16 +-
services/crunch-run/crunchrun.go | 9 +
services/crunch-run/crunchrun_test.go | 22 +-
.../arvnodeman/computenode/dispatch/slurm.py | 2 +-
.../arvnodeman/computenode/driver/ec2.py | 2 +-
services/nodemanager/arvnodeman/config.py | 6 +-
services/nodemanager/arvnodeman/jobqueue.py | 6 +-
services/nodemanager/arvnodeman/nodelist.py | 2 +-
services/nodemanager/doc/ec2.example.cfg | 12 ++
services/nodemanager/setup.py | 4 +-
services/nodemanager/tests/integration_test.py | 2 +-
.../tests/test_computenode_dispatch_slurm.py | 14 +-
.../tests/test_computenode_driver_ec2.py | 4 +-
services/nodemanager/tests/test_config.py | 14 +-
services/nodemanager/tests/test_jobqueue.py | 12 +-
services/nodemanager/tests/test_nodelist.py | 4 +-
services/nodemanager/tests/testutil.py | 4 +-
94 files changed, 2346 insertions(+), 632 deletions(-)
create mode 100644 doc/admin/activation.html.textile.liquid
create mode 100644 doc/admin/spot-instances.html.textile.liquid
create mode 100644 doc/install/arvados-on-kubernetes-GKE.html.textile.liquid
create mode 100644 doc/install/arvados-on-kubernetes-minikube.html.textile.liquid
create mode 100644 doc/install/arvados-on-kubernetes.html.textile.liquid
create mode 100644 sdk/R/R/zzz.R
create mode 100644 sdk/cwl/arvados_cwl/context.py
create mode 100644 sdk/cwl/arvados_cwl/util.py
create mode 100644 sdk/cwl/tests/makes_intermediates/echo.cwl
copy apps/workbench/app/mailers/.gitkeep => sdk/cwl/tests/makes_intermediates/hello1.txt (100%)
create mode 100644 sdk/cwl/tests/makes_intermediates/run_in_single.cwl
create mode 100644 sdk/cwl/tests/makes_intermediates/subwf.cwl
create mode 100644 sdk/cwl/tests/test_util.py
copy sdk/cwl/tests/wf/{submit_wf.cwl => submit_wf_runner_resources.cwl} (81%)
create mode 100644 sdk/go/arvados/byte_size.go
create mode 100644 sdk/go/arvados/byte_size_test.go
create mode 100644 sdk/go/arvados/config_test.go
create mode 100644 services/api/test/unit/update_priority_test.rb
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Those revisions listed above that are new to this repository have
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commit 4369714821950366db98a54e4b62fdb5d09951a6
Author: Tom Clegg <tclegg at veritasgenetics.com>
Date: Wed Jul 11 09:27:12 2018 -0400
13497: 13779: Forward Host header, and don't follow redirects.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg at veritasgenetics.com>
diff --git a/lib/controller/handler.go b/lib/controller/handler.go
index 59c2f2a61..92ded6301 100644
--- a/lib/controller/handler.go
+++ b/lib/controller/handler.go
@@ -47,6 +47,11 @@ func (h *Handler) setup() {
})
mux.Handle("/", http.HandlerFunc(h.proxyRailsAPI))
h.handlerStack = mux
+
+ // Changing the global isn't the right way to do this, but a
+ // proper solution would conflict with an impending 13493
+ // merge anyway, so this will do for now.
+ arvados.InsecureHTTPClient.CheckRedirect = func(*http.Request, []*http.Request) error { return http.ErrUseLastResponse }
}
// headers that shouldn't be forwarded when proxying. See
@@ -101,6 +106,7 @@ func (h *Handler) proxyRailsAPI(w http.ResponseWriter, reqIn *http.Request) {
reqOut := (&http.Request{
Method: reqIn.Method,
URL: urlOut,
+ Host: reqIn.Host,
Header: hdrOut,
Body: reqIn.Body,
}).WithContext(ctx)
diff --git a/lib/controller/handler_test.go b/lib/controller/handler_test.go
index 981ad7ab9..eb947ea36 100644
--- a/lib/controller/handler_test.go
+++ b/lib/controller/handler_test.go
@@ -120,3 +120,11 @@ func (s *HandlerSuite) TestProxyNotFound(c *check.C) {
c.Check(err, check.IsNil)
c.Check(jresp["errors"], check.FitsTypeOf, []interface{}{})
}
+
+func (s *HandlerSuite) TestProxyRedirect(c *check.C) {
+ req := httptest.NewRequest("GET", "https://example.org:1234/login?return_to=foo", nil)
+ resp := httptest.NewRecorder()
+ s.handler.ServeHTTP(resp, req)
+ c.Check(resp.Code, check.Equals, http.StatusFound)
+ c.Check(resp.Header().Get("Location"), check.Matches, `https://example\.org:1234/auth/joshid\?return_to=foo&?`)
+}
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