[ARVADOS] updated: be4e5f225cf1615504ee2c1feb0f200d6904716c

git at public.curoverse.com git at public.curoverse.com
Mon Aug 10 14:16:57 EDT 2015


Summary of changes:
 apps/workbench/Gemfile.lock                        |   3 -
 .../app/controllers/actions_controller.rb          |  10 +
 apps/workbench/app/controllers/users_controller.rb |  19 +-
 .../app/helpers/pipeline_instances_helper.rb       |   4 +-
 apps/workbench/app/models/arvados_base.rb          |   4 +
 apps/workbench/app/models/user.rb                  |   3 +
 .../application/_delete_object_button.html.erb     |   2 +-
 .../views/application/_show_home_button.html.erb   |   3 +
 .../app/views/application/_show_recent.html.erb    |  18 +-
 apps/workbench/app/views/layouts/body.html.erb     |  30 +-
 .../notifications/_ssh_key_notification.html.erb   |   5 +-
 .../pipeline_instances/_running_component.html.erb |  16 +-
 .../_show_components_running.html.erb              |  24 +-
 ...rent_token.html.erb => _current_token.html.erb} |   5 +-
 .../app/views/users/_manage_account.html.erb       |  22 -
 ...epositories.html.erb => _repositories.html.erb} |   6 +-
 ...manage_ssh_keys.html.erb => _ssh_keys.html.erb} |   9 +-
 ...achines.html.erb => _virtual_machines.html.erb} |  14 +-
 .../app/views/users/current_token.html.erb         |   1 +
 .../app/views/users/manage_account.html.erb        |   1 -
 .../app/views/users/repositories.html.erb          |   2 +
 apps/workbench/app/views/users/ssh_keys.html.erb   |   2 +
 .../app/views/users/virtual_machines.html.erb      |   1 +
 .../app/views/virtual_machines/webshell.html.erb   |   4 +-
 apps/workbench/config/routes.rb                    |   5 +-
 .../test/controllers/actions_controller_test.rb    |  39 ++
 .../controllers/application_controller_test.rb     |  41 ++
 .../test/controllers/projects_controller_test.rb   |  10 +
 .../test/controllers/users_controller_test.rb      |   4 +-
 .../test/integration/application_layout_test.rb    |  14 +-
 .../test/integration/pipeline_instances_test.rb    |   2 +-
 .../test/integration/user_profile_test.rb          |   5 +-
 ..._account_test.rb => user_settings_menu_test.rb} |  88 +++-
 doc/_config.yml                                    |   8 +-
 doc/_includes/_arv_copy_expectations.liquid        |   5 +-
 doc/_includes/_install_git_curl.liquid             |  13 +
 doc/_includes/_install_postgres.liquid             |  22 +
 .../_install_ruby_and_bundler.liquid}              |  19 +-
 doc/_includes/_ssh_addkey.liquid                   |   4 +-
 .../create-standard-objects.html.textile.liquid    |  31 +-
 doc/install/install-api-server.html.textile.liquid | 183 +++++---
 .../install-arv-git-httpd.html.textile.liquid      | 325 +++++++++++++-
 .../install-compute-node.html.textile.liquid       |  24 +-
 .../install-crunch-dispatch.html.textile.liquid    |  45 +-
 doc/install/install-docker.html.textile.liquid     |   6 +-
 doc/install/install-keepproxy.html.textile.liquid  |   6 +-
 doc/install/install-keepstore.html.textile.liquid  |   2 +-
 ...nstall-manual-prerequisites.html.textile.liquid |  28 +-
 .../install-shell-server.html.textile.liquid       |  16 +-
 doc/install/install-sso.html.textile.liquid        | 299 ++++++++-----
 .../install-workbench-app.html.textile.liquid      |  39 +-
 doc/sdk/cli/install.html.textile.liquid            |   8 +-
 doc/sdk/cli/subcommands.html.textile.liquid        |   2 +-
 doc/sdk/perl/index.html.textile.liquid             |   2 +-
 .../vm-login-with-webshell.html.textile.liquid     |   4 +-
 doc/user/reference/api-tokens.html.textile.liquid  |   4 +-
 doc/user/topics/arv-copy.html.textile.liquid       |   2 +-
 doc/user/topics/arv-run.html.textile.liquid        |   2 +-
 .../add-new-repository.html.textile.liquid         |   6 +-
 .../running-external-program.html.textile.liquid   |  17 +-
 .../tutorial-submit-job.html.textile.liquid        |   6 +-
 docker/api/Dockerfile                              |   4 +-
 docker/api/setup-gitolite.sh.in                    |   2 +-
 sdk/cli/bin/crunch-job                             |  39 +-
 sdk/cli/test/binstub_clean_fail/mount              |   3 +
 sdk/cli/test/binstub_docker_noop/docker.io         |   2 +
 sdk/cli/test/binstub_sanity_check/docker.io        |   2 +
 sdk/cli/test/binstub_sanity_check/true             |   2 +
 sdk/cli/test/test_arv-collection-create.rb         |   2 -
 sdk/cli/test/test_arv-get.rb                       |  42 +-
 sdk/cli/test/test_arv-put.rb                       |  26 --
 sdk/cli/test/test_arv-run-pipeline-instance.rb     |   2 -
 sdk/cli/test/test_arv-tag.rb                       |   2 +-
 sdk/cli/test/test_crunch-job.rb                    | 126 ++++++
 sdk/perl/Makefile.PL                               |   7 +-
 sdk/python/arvados/arvfile.py                      |   4 +-
 sdk/python/arvados/commands/arv_copy.py            |  51 ++-
 sdk/python/arvados/commands/put.py                 |  19 +-
 sdk/python/arvados/commands/run.py                 |   9 +-
 sdk/python/arvados/events.py                       |  60 ++-
 sdk/python/arvados/keep.py                         |   5 +-
 sdk/python/arvados/retry.py                        |   3 +-
 sdk/python/bin/arv-get                             |  73 +--
 sdk/python/tests/test_retry.py                     |   6 +-
 sdk/python/tests/test_websockets.py                | 136 +++---
 .../arvados/v1/repositories_controller.rb          | 136 ++++--
 services/api/app/models/arvados_model.rb           |  11 +-
 services/api/app/models/authorized_key.rb          |   4 +-
 services/api/app/models/collection.rb              |  18 +-
 services/api/app/models/commit.rb                  |  32 +-
 .../views/user_notifier/account_is_setup.text.erb  |   4 +-
 services/api/config/application.default.yml        | 488 +++++++++++----------
 services/api/config/application.yml.example        |  31 +-
 .../{database.yml.sample => database.yml.example}  |   0
 .../initializers/hardcoded_api_tokens.rb.example   |   3 -
 services/api/lib/eventbus.rb                       |  11 +-
 .../api/script/arvados-git-sync.rb                 |   7 +-
 services/api/script/crunch-dispatch.rb             |   7 +
 services/api/test/fixtures/humans.yml              |   1 +
 services/api/test/fixtures/links.yml               |  14 +
 services/api/test/fixtures/users.yml               |   1 +
 .../arvados/v1/collections_controller_test.rb      |  78 ++++
 .../arvados/v1/repositories_controller_test.rb     |  97 +++-
 .../functional/arvados/v1/users_controller_test.rb |   3 +-
 services/api/test/integration/websocket_test.rb    |  47 +-
 services/api/test/unit/authorized_key_test.rb      |  46 +-
 services/api/test/unit/collection_test.rb          |  60 +++
 services/arv-git-httpd/auth_handler.go             |  16 +-
 services/arv-git-httpd/server_test.go              |  15 +
 services/datamanager/datamanager.go                |  44 +-
 services/datamanager/keep/keep.go                  |  84 +++-
 services/datamanager/keep/keep_test.go             |  81 ++++
 services/datamanager/summary/pull_list.go          |   6 +-
 services/datamanager/summary/pull_list_test.go     |  81 ++--
 services/datamanager/summary/trash_list.go         |  60 +++
 services/datamanager/summary/trash_list_test.go    |  76 ++++
 services/fuse/arvados_fuse/__init__.py             |  64 ++-
 services/fuse/arvados_fuse/fusedir.py              |  12 +-
 services/fuse/tests/mount_test_base.py             |   4 +-
 services/fuse/tests/test_mount.py                  |  37 +-
 services/keepstore/trash_worker.go                 |   8 +-
 121 files changed, 2767 insertions(+), 1091 deletions(-)
 create mode 100644 apps/workbench/app/views/application/_show_home_button.html.erb
 rename apps/workbench/app/views/users/{_manage_current_token.html.erb => _current_token.html.erb} (69%)
 delete mode 100644 apps/workbench/app/views/users/_manage_account.html.erb
 rename apps/workbench/app/views/users/{_manage_repositories.html.erb => _repositories.html.erb} (83%)
 rename apps/workbench/app/views/users/{_manage_ssh_keys.html.erb => _ssh_keys.html.erb} (91%)
 rename apps/workbench/app/views/users/{_manage_virtual_machines.html.erb => _virtual_machines.html.erb} (92%)
 create mode 100644 apps/workbench/app/views/users/current_token.html.erb
 delete mode 100644 apps/workbench/app/views/users/manage_account.html.erb
 create mode 100644 apps/workbench/app/views/users/repositories.html.erb
 create mode 100644 apps/workbench/app/views/users/ssh_keys.html.erb
 create mode 100644 apps/workbench/app/views/users/virtual_machines.html.erb
 rename apps/workbench/test/integration/{user_manage_account_test.rb => user_settings_menu_test.rb} (65%)
 create mode 100644 doc/_includes/_install_git_curl.liquid
 create mode 100644 doc/_includes/_install_postgres.liquid
 rename doc/{install/install-manual-prerequisites-ruby.html.textile.liquid => _includes/_install_ruby_and_bundler.liquid} (85%)
 create mode 100755 sdk/cli/test/binstub_clean_fail/mount
 create mode 100755 sdk/cli/test/binstub_docker_noop/docker.io
 create mode 100755 sdk/cli/test/binstub_sanity_check/docker.io
 create mode 100755 sdk/cli/test/binstub_sanity_check/true
 create mode 100644 sdk/cli/test/test_crunch-job.rb
 rename services/api/config/{database.yml.sample => database.yml.example} (100%)
 delete mode 100644 services/api/config/initializers/hardcoded_api_tokens.rb.example
 rename docker/api/update-gitolite.rb => services/api/script/arvados-git-sync.rb (96%)
 create mode 100644 services/api/test/fixtures/humans.yml
 create mode 100644 services/datamanager/keep/keep_test.go
 create mode 100644 services/datamanager/summary/trash_list.go
 create mode 100644 services/datamanager/summary/trash_list_test.go

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commit be4e5f225cf1615504ee2c1feb0f200d6904716c
Merge: 12c47d0 e0213cb
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Aug 10 14:13:45 2015 -0400

    Merge branch 'master' into 5824-go-sdk
    
    Conflicts:
    	services/arv-git-httpd/auth_handler.go

diff --cc services/arv-git-httpd/auth_handler.go
index 0fb1567,b284f19..dccbe7f
--- a/services/arv-git-httpd/auth_handler.go
+++ b/services/arv-git-httpd/auth_handler.go
@@@ -34,11 -52,25 +34,25 @@@ func (h *authHandler) ServeHTTP(wOrig h
  			w.WriteHeader(statusCode)
  			w.Write([]byte(statusText))
  		}
- 		httpserver.Log(r.RemoteAddr, apiToken, w.WroteStatus(), statusText, repoName, r.Method, r.URL.Path)
+ 
 -    // If the given password is a valid token, log the first 10 characters of the token.
 -    // Otherwise: log the string <invalid> if a password is given, else an empty string.
++		// If the given password is a valid token, log the
++		// first 10 characters of the token.  Otherwise: log
++		// the string <invalid> if a password is given, else
++		// an empty string.
+ 		passwordToLog := ""
+ 		if statusCode == 401 || strings.Contains(statusText, "Unauthorized") {
 -			if len(password) > 0 {
++			if len(apiToken) > 0 {
+ 				passwordToLog = "<invalid>"
+ 			}
+ 		} else {
 -			passwordToLog = password[0:10]
++			passwordToLog = apiToken[0:10]
+ 		}
+ 
 -		log.Println(quoteStrings(r.RemoteAddr, username, passwordToLog, wroteStatus, statusText, repoName, r.Method, r.URL.Path)...)
++		httpserver.Log(r.RemoteAddr, passwordToLog, w.WroteStatus(), statusText, repoName, r.Method, r.URL.Path)
  	}()
  
 -	// HTTP request username is logged, but unused. Password is an
 -	// Arvados API token.
 -	username, password, ok := BasicAuth(r)
 -	if !ok || username == "" || password == "" {
 +	creds := auth.NewCredentialsFromHTTPRequest(r)
 +	if len(creds.Tokens) == 0 {
  		statusCode, statusText = http.StatusUnauthorized, "no credentials provided"
  		w.Header().Add("WWW-Authenticate", "Basic realm=\"git\"")
  		return

-----------------------------------------------------------------------


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