arvados.git
10 years agoMerge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers
Tim Pierce [Thu, 10 Apr 2014 22:45:00 +0000 (18:45 -0400)]
Merge branch '2449-keep-write-blocks' into 2449-keep-index-status-handlers

Conflicts:
services/keep/keep.go

10 years agoAdded status.json handler. (refs #2561)
Tim Pierce [Thu, 10 Apr 2014 22:43:01 +0000 (18:43 -0400)]
Added status.json handler. (refs #2561)

10 years agoMerge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Thu, 10 Apr 2014 20:34:45 +0000 (16:34 -0400)]
Merge branch 'master' into 2449-keep-write-blocks

10 years agoUpdate for code review (refs #2292).
Tim Pierce [Thu, 10 Apr 2014 20:31:47 +0000 (16:31 -0400)]
Update for code review (refs #2292).

* Use ioutil.TempFile to write new blocks, renaming to the correct
  name upon success.

* PutBlock should overwrite corrupt blocks, not report a collision.

* Get free disk space from syscall.Statfs, not `df`.

10 years agoAdded /index handlers. (refs #2561)
Tim Pierce [Wed, 9 Apr 2014 22:03:19 +0000 (18:03 -0400)]
Added /index handlers. (refs #2561)

10 years agoapi: Give all Job fixtures script_versions.
Brett Smith [Wed, 9 Apr 2014 19:34:16 +0000 (15:34 -0400)]
api: Give all Job fixtures script_versions.

Workbench tries to call to_sym on these versions, and hiccups if it's
nil.  This makes it easier to run integration tests, whether
automatically or by hand.

10 years agoTrim newline from output hash emerging from `arv keep put`.
Tom Clegg [Wed, 9 Apr 2014 03:45:12 +0000 (23:45 -0400)]
Trim newline from output hash emerging from `arv keep put`.

10 years agoFix tests: make sure system_user exists before making "pre-test users" list
Tom Clegg [Wed, 9 Apr 2014 03:32:27 +0000 (23:32 -0400)]
Fix tests: make sure system_user exists before making "pre-test users" list

10 years agoFix permission error when adding system_group->new_user permission link.
Tom Clegg [Tue, 8 Apr 2014 23:50:46 +0000 (19:50 -0400)]
Fix permission error when adding system_group->new_user permission link.

10 years agoChange password placeholder to something db:load_config can parse.
Tom Clegg [Tue, 8 Apr 2014 23:08:33 +0000 (19:08 -0400)]
Change password placeholder to something db:load_config can parse.

10 years agoMerge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Tue, 8 Apr 2014 18:11:24 +0000 (14:11 -0400)]
Merge branch 'master' into 2449-keep-write-blocks

10 years agoMove the javascript into a js file instead of using <script> tag in html file.
radhika chippada [Tue, 8 Apr 2014 16:00:32 +0000 (12:00 -0400)]
Move the javascript into a js file instead of using <script> tag in html file.

10 years agoRemove trailing white spaces.
radhika chippada [Tue, 8 Apr 2014 14:40:31 +0000 (10:40 -0400)]
Remove trailing white spaces.

10 years agoAdd paste event check for submit button validation
radhika chippada [Tue, 8 Apr 2014 14:29:40 +0000 (10:29 -0400)]
Add paste event check for submit button validation

10 years agoUse bootstrap/theme style defaults for user setup modal and form.
Tom Clegg [Tue, 8 Apr 2014 05:55:17 +0000 (01:55 -0400)]
Use bootstrap/theme style defaults for user setup modal and form.

10 years agoReset form fields on cancel.
radhika chippada [Mon, 7 Apr 2014 19:04:06 +0000 (15:04 -0400)]
Reset form fields on cancel.

10 years agoSubmit
radhika chippada [Mon, 7 Apr 2014 18:44:49 +0000 (14:44 -0400)]
Submit

10 years agoBootstrap modal css updated to include only what is needed.
radhika chippada [Mon, 7 Apr 2014 18:03:01 +0000 (14:03 -0400)]
Bootstrap modal css updated to include only what is needed.

10 years agoAdd header and footer to the setup user modal
radhika chippada [Mon, 7 Apr 2014 15:58:08 +0000 (11:58 -0400)]
Add header and footer to the setup user modal

10 years agoDocument capybara-webkit qt dependencies, and add phantomjs recipe.
Tom Clegg [Fri, 4 Apr 2014 21:21:45 +0000 (17:21 -0400)]
Document capybara-webkit qt dependencies, and add phantomjs recipe.

10 years agoAdd email format validation to the input text field in the setup modal.
radhika chippada [Fri, 4 Apr 2014 19:45:53 +0000 (15:45 -0400)]
Add email format validation to the input text field in the setup modal.

10 years agoDuring setup of an existing user, create oid login permission, if it does not already...
radhika chippada [Fri, 4 Apr 2014 18:53:42 +0000 (14:53 -0400)]
During setup of an existing user, create oid login permission, if it does not already exist.

10 years agoNeed to remove the user's "all users" group read permission during unsetup.
radhika chippada [Fri, 4 Apr 2014 17:36:01 +0000 (13:36 -0400)]
Need to remove the user's "all users" group read permission during unsetup.
This shortcoming became apparent during testing when "is_invited" flag is checked.

10 years agoUse webkit driver for Capybara instead of selenium for tests that need dialog handling.
radhika chippada [Fri, 4 Apr 2014 14:45:14 +0000 (10:45 -0400)]
Use webkit driver for Capybara instead of selenium for tests that need dialog handling.

10 years agoAdded integration tests for create new user, setup and unsetup existing user. The...
radhika chippada [Fri, 4 Apr 2014 02:41:42 +0000 (22:41 -0400)]
Added integration tests for create new user, setup and unsetup existing user. The tests use selenium driver without headless. Hence, we see the browser while these tests are running.

Next step is to use headless to hide the browser during test execution.

10 years agoIntegration test for setup user
radhika chippada [Thu, 3 Apr 2014 18:23:10 +0000 (14:23 -0400)]
Integration test for setup user

10 years agoSubmit button enabling revisited
radhika chippada [Thu, 3 Apr 2014 15:05:47 +0000 (11:05 -0400)]
Submit button enabling revisited

10 years agoSubmit button enabled when existing user
radhika chippada [Thu, 3 Apr 2014 11:39:06 +0000 (07:39 -0400)]
Submit button enabled when existing user

10 years agopopup submit button
radhika chippada [Thu, 3 Apr 2014 11:17:03 +0000 (07:17 -0400)]
popup submit button

10 years agoGet the default openid_prefix from config.
radhika chippada [Thu, 3 Apr 2014 01:08:03 +0000 (21:08 -0400)]
Get the default openid_prefix from config.

10 years agoLook for repo_name in VM link
radhika chippada [Thu, 3 Apr 2014 00:56:54 +0000 (20:56 -0400)]
Look for repo_name in VM link

10 years agoRequire only email and openid prefix in the setup popup. The other fields are optional.
radhika chippada [Thu, 3 Apr 2014 00:28:14 +0000 (20:28 -0400)]
Require only email and openid prefix in the setup popup. The other fields are optional.

10 years agoNew user creation using setup action is working
radhika chippada [Wed, 2 Apr 2014 23:51:45 +0000 (19:51 -0400)]
New user creation using setup action is working

10 years ago"Add a new user" link uses setup method to create a "loaded" user.
radhika chippada [Wed, 2 Apr 2014 22:52:04 +0000 (18:52 -0400)]
"Add a new user" link uses setup method to create a "loaded" user.

10 years agoMinor UI tweaks
radhika chippada [Wed, 2 Apr 2014 16:57:13 +0000 (12:57 -0400)]
Minor UI tweaks

10 years agoDisable submit button until all input fields are filled in.
radhika chippada [Wed, 2 Apr 2014 04:04:16 +0000 (00:04 -0400)]
Disable submit button until all input fields are filled in.

10 years agoAdded bootstrap css
radhika chippada [Tue, 1 Apr 2014 21:21:12 +0000 (17:21 -0400)]
Added bootstrap css

10 years agoPre-fill form fields with previous selections where applicable.
radhika chippada [Tue, 1 Apr 2014 20:26:58 +0000 (16:26 -0400)]
Pre-fill form fields with previous selections where applicable.

10 years agoVirtual machines in a dropdown option in setup popup
radhika chippada [Tue, 1 Apr 2014 18:38:50 +0000 (14:38 -0400)]
Virtual machines in a dropdown option in setup popup

10 years agoPass all parameters to the setup method
radhika chippada [Tue, 1 Apr 2014 17:47:11 +0000 (13:47 -0400)]
Pass all parameters to the setup method

10 years agoMultiple input elements in popup
radhika chippada [Tue, 1 Apr 2014 15:51:03 +0000 (11:51 -0400)]
Multiple input elements in popup

10 years agoPopup closes on submit
radhika chippada [Tue, 1 Apr 2014 03:46:42 +0000 (23:46 -0400)]
Popup closes on submit

10 years agoWorking on setup popup
radhika chippada [Mon, 31 Mar 2014 21:54:32 +0000 (17:54 -0400)]
Working on setup popup

10 years agoSetup popup display
radhika chippada [Mon, 31 Mar 2014 14:53:20 +0000 (10:53 -0400)]
Setup popup display

10 years agoWorking on setup popup
radhika chippada [Mon, 31 Mar 2014 01:15:45 +0000 (21:15 -0400)]
Working on setup popup

10 years agoAdd a setup action to users controller and user model
radhika chippada [Sun, 30 Mar 2014 22:07:46 +0000 (18:07 -0400)]
Add a setup action to users controller and user model

10 years agoConfirm dialog check commented our for now. Why is that I can't intercept the dialog...
radhika chippada [Fri, 28 Mar 2014 19:44:31 +0000 (15:44 -0400)]
Confirm dialog check commented our for now. Why is that I can't intercept the dialog and instead why is the  OK button clicked automatically?

10 years agoAdd users integration test class. Beginnings of setup and unsetup method tests.
radhika chippada [Fri, 28 Mar 2014 19:21:05 +0000 (15:21 -0400)]
Add users integration test class. Beginnings of setup and unsetup method tests.

10 years agoCheck for MD5 collisions and corrupt blocks. (refs #2292)
Tim Pierce [Tue, 8 Apr 2014 04:04:29 +0000 (00:04 -0400)]
Check for MD5 collisions and corrupt blocks. (refs #2292)

10 years agoMerge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Mon, 7 Apr 2014 19:51:41 +0000 (15:51 -0400)]
Merge branch 'master' into 2449-keep-write-blocks

10 years agoAdded IsFull() to check for free space before writing. (refs #2292)
Tim Pierce [Mon, 7 Apr 2014 19:49:51 +0000 (15:49 -0400)]
Added IsFull() to check for free space before writing. (refs #2292)

10 years agoRemove Ruby 2.1.0 dependency by using Hash[x] instead of x.to_h.
Tom Clegg [Fri, 4 Apr 2014 21:25:38 +0000 (17:25 -0400)]
Remove Ruby 2.1.0 dependency by using Hash[x] instead of x.to_h.

10 years agoMerge branch 'master' into 2449-keep-write-blocks
Tim Pierce [Fri, 4 Apr 2014 19:51:43 +0000 (15:51 -0400)]
Merge branch 'master' into 2449-keep-write-blocks

10 years agoPutBlock saves a block on only the first available volume (refs #2292)
Tim Pierce [Fri, 4 Apr 2014 19:42:13 +0000 (15:42 -0400)]
PutBlock saves a block on only the first available volume (refs #2292)

Per code review: Keep stores a block on only one disk at a time.
Updated PutBlock, and PutBlock/GetBlock unit tests, appropriately.

10 years agoFix copy/paste error.
Tom Clegg [Fri, 4 Apr 2014 14:26:23 +0000 (10:26 -0400)]
Fix copy/paste error.

10 years agoFix $keep variable scope (refs #2221)
Tim Pierce [Thu, 3 Apr 2014 19:52:49 +0000 (15:52 -0400)]
Fix $keep variable scope (refs #2221)

10 years agoMerge branch '2221-complete-docker' (closes #2325, closes #2221)
Tim Pierce [Thu, 3 Apr 2014 19:51:48 +0000 (15:51 -0400)]
Merge branch '2221-complete-docker' (closes #2325, closes #2221)

Conflicts:
.gitignore

10 years agoSemicolon fix (refs #2325, refs #2221).
Tim Pierce [Thu, 3 Apr 2014 19:47:44 +0000 (15:47 -0400)]
Semicolon fix (refs #2325, refs #2221).

10 years agoMerge branch '2509-rake-linkchecker'
Ward Vandewege [Thu, 3 Apr 2014 19:27:51 +0000 (15:27 -0400)]
Merge branch '2509-rake-linkchecker'

10 years agoUse a simple 'open' for fetch_block (freeing up an extra filehandle). refs #2325...
Tim Pierce [Thu, 3 Apr 2014 19:25:35 +0000 (15:25 -0400)]
Use a simple 'open' for fetch_block (freeing up an extra filehandle). refs #2325, refs #2221

10 years agoResolving style comments from #2325. (refs #2325, refs #2221)
Tim Pierce [Thu, 3 Apr 2014 19:08:15 +0000 (15:08 -0400)]
Resolving style comments from #2325. (refs #2325, refs #2221)

10 years ago* README: remove numbers in headings
Ward Vandewege [Thu, 3 Apr 2014 18:27:16 +0000 (14:27 -0400)]
* README: remove numbers in headings

* linkchecker: only check file:// links

* epydoc: run against the local source tree, not against whatever
  version of the python 'arvados' package is installed

* generate: re-run epydoc on every generation

* generate: do not fail to include the epydoc output files if they are
  generated in the current run (which they now always are)

10 years agoUse quotemeta to protect shell escapes (refs #2221, #2325)
Tim Pierce [Thu, 3 Apr 2014 18:22:10 +0000 (14:22 -0400)]
Use quotemeta to protect shell escapes (refs #2221, #2325)

10 years agoSet umask to 022 when creating config files. (refs #2221)
Tim Pierce [Thu, 3 Apr 2014 18:00:16 +0000 (14:00 -0400)]
Set umask to 022 when creating config files. (refs #2221)

10 years agodocker: Install staged source on Docker images.
Brett Smith [Wed, 2 Apr 2014 20:55:24 +0000 (16:55 -0400)]
docker: Install staged source on Docker images.

A separate build step to stage source makes it easier for us to fix
permissions and do other clean-up before installing it in a Docker
image.  It also reduces code redundancy; for example, builders don't
have to worry about excluding log and tmp directories.

10 years agodocker: Tolerate existing tmp in api-image.
Brett Smith [Wed, 2 Apr 2014 20:41:50 +0000 (16:41 -0400)]
docker: Tolerate existing tmp in api-image.

10 years agodocker: `chmod go=rX` on generated files.
Brett Smith [Wed, 2 Apr 2014 20:33:59 +0000 (16:33 -0400)]
docker: `chmod go=rX` on generated files.

That's not how this is implemented, but the end result should be the
same.

10 years agodocker: Don't try shell expansion in Makefile.
Brett Smith [Wed, 2 Apr 2014 19:32:12 +0000 (15:32 -0400)]
docker: Don't try shell expansion in Makefile.

The original syntax, at least, is not supported.

10 years agodocker: Improve build.sh's Makefile finding.
Brett Smith [Wed, 2 Apr 2014 18:04:48 +0000 (14:04 -0400)]
docker: Improve build.sh's Makefile finding.

10 years agodoc: Add rake linkchecker task, and document it in the README file
Ward Vandewege [Wed, 2 Apr 2014 16:58:00 +0000 (12:58 -0400)]
doc: Add rake linkchecker task, and document it in the README file

10 years agoMerge branch '2209-correct-items-available'
Tom Clegg [Wed, 2 Apr 2014 16:40:08 +0000 (12:40 -0400)]
Merge branch '2209-correct-items-available'

closes #2209

10 years agoFix counting results in test case (count != size for an ActiveRelation).
Tom Clegg [Wed, 2 Apr 2014 16:39:52 +0000 (12:39 -0400)]
Fix counting results in test case (count != size for an ActiveRelation).

10 years agoMerge branch 'master' into 2209-correct-items-available
Tom Clegg [Wed, 2 Apr 2014 16:30:44 +0000 (12:30 -0400)]
Merge branch 'master' into 2209-correct-items-available

10 years agoReally check for duplicate items returned, instead of just calling a
Tom Clegg [Wed, 2 Apr 2014 16:30:12 +0000 (12:30 -0400)]
Really check for duplicate items returned, instead of just calling a
variable unique_uuids.

10 years agodoc: Fix Keep links in tutorial-job1.
Brett Smith [Wed, 2 Apr 2014 14:12:37 +0000 (10:12 -0400)]
doc: Fix Keep links in tutorial-job1.

10 years agoMerge branch '2470-doc-refresh'.
Brett Smith [Wed, 2 Apr 2014 14:05:01 +0000 (10:05 -0400)]
Merge branch '2470-doc-refresh'.

Closes #2470, #2490.

10 years agodoc: Implement Tom's suggested improvements.
Brett Smith [Tue, 1 Apr 2014 21:37:07 +0000 (17:37 -0400)]
doc: Implement Tom's suggested improvements.

Refs #2470.

10 years agodoc: tutorial-job1 updates and style tweaks.
Brett Smith [Mon, 31 Mar 2014 13:46:50 +0000 (09:46 -0400)]
doc: tutorial-job1 updates and style tweaks.

The major change here is that we set no_reuse on the job, to avoid
confusing people by using results from previous tutorial runs.  These
updates also reflect some minor changes in the Workbench UI.

10 years agodoc: job-and-pipeline-ref grammar fixes.
Brett Smith [Fri, 28 Mar 2014 21:23:40 +0000 (17:23 -0400)]
doc: job-and-pipeline-ref grammar fixes.

10 years agodoc: Keep topic style tweaks.
Brett Smith [Fri, 28 Mar 2014 21:06:19 +0000 (17:06 -0400)]
doc: Keep topic style tweaks.

10 years agodoc: Fix typos in tutorial-parallel.
Brett Smith [Fri, 28 Mar 2014 20:57:09 +0000 (16:57 -0400)]
doc: Fix typos in tutorial-parallel.

10 years agodoc: tutorial-job-debug update and style.
Brett Smith [Fri, 28 Mar 2014 20:51:36 +0000 (16:51 -0400)]
doc: tutorial-job-debug update and style.

* Jobs now require a "repository" parameter.
* Use environment variables to specify the job script.

10 years agodoc: Make running-pipeline-command up-to-date.
Brett Smith [Fri, 28 Mar 2014 19:47:52 +0000 (15:47 -0400)]
doc: Make running-pipeline-command up-to-date.

* @arv pipeline run@ now requires @--run-here@.
* Pipelines are now under Activity in Workbench navigation.
* The format of the example output has changed, along with all the
  Keep hashes.

10 years agodoc: Highlight "you" in reference JSON.
Brett Smith [Fri, 28 Mar 2014 14:31:59 +0000 (10:31 -0400)]
doc: Highlight "you" in reference JSON.

Since this reference provides users with raw example JSON, and doesn't
tell them to write it with @cat@, we can't rely on shell variable
expansion here.

10 years agodoc: Use $USER in tutorial JSON.
Brett Smith [Mon, 31 Mar 2014 13:51:42 +0000 (09:51 -0400)]
doc: Use $USER in tutorial JSON.

The tutorial encourages users to copy and paste command text.
However, most of the JSON needs to have a user-specific value for
"repository", which is easy to overlook.  Since we're telling users to
save JSON with @cat@, we can take advantage of shell variable
expansion to make the right thing happen automatically.

I added accompanying notes to help explain what's going on for people
who aren't copying instructions so literally.

Conflicts:
doc/user/tutorials/tutorial-firstscript.html.textile.liquid
doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid

10 years agodoc: Tweak running-external-program style.
Brett Smith [Thu, 27 Mar 2014 20:00:09 +0000 (16:00 -0400)]
doc: Tweak running-external-program style.

10 years agodoc: tutorial-new-pipeline clarity.
Brett Smith [Mon, 31 Mar 2014 13:50:55 +0000 (09:50 -0400)]
doc: tutorial-new-pipeline clarity.

I renamed the "filter" job to "do_filter" to help disambiguate it a
little from "0-filter.py".

Conflicts:
doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid

10 years agodoc: tutorial-firstscript style consistency.
Brett Smith [Mon, 31 Mar 2014 13:50:01 +0000 (09:50 -0400)]
doc: tutorial-firstscript style consistency.

Conflicts:
doc/user/tutorials/tutorial-firstscript.html.textile.liquid

10 years agodoc: tutorial-pipeline-workbench style+clarity.
Brett Smith [Thu, 27 Mar 2014 18:01:27 +0000 (14:01 -0400)]
doc: tutorial-pipeline-workbench style+clarity.

10 years agodoc: Fix tutorial-keep typos and consistency.
Brett Smith [Thu, 27 Mar 2014 16:46:19 +0000 (12:46 -0400)]
doc: Fix tutorial-keep typos and consistency.

10 years agodoc: Fix api-tokens typos and consistency.
Brett Smith [Thu, 27 Mar 2014 16:15:51 +0000 (12:15 -0400)]
doc: Fix api-tokens typos and consistency.

10 years agodoc: Fix ssh-access typos and consistency.
Brett Smith [Thu, 27 Mar 2014 15:56:55 +0000 (11:56 -0400)]
doc: Fix ssh-access typos and consistency.

10 years agodoc: Style and consistency in user/index.
Brett Smith [Thu, 27 Mar 2014 15:09:00 +0000 (11:09 -0400)]
doc: Style and consistency in user/index.

10 years agoDoc fixes.
Tim Pierce [Wed, 2 Apr 2014 05:26:33 +0000 (01:26 -0400)]
Doc fixes.

10 years agoMerge branch '2447-fix-workbench-search'
Tom Clegg [Wed, 2 Apr 2014 02:41:11 +0000 (22:41 -0400)]
Merge branch '2447-fix-workbench-search'

closes #2447

10 years agoFix searching on tables with no "name" column. Take care not to use
Tom Clegg [Wed, 2 Apr 2014 02:16:43 +0000 (22:16 -0400)]
Fix searching on tables with no "name" column. Take care not to use
string operators on incompatible column types when applying
where/filters.

10 years agoLoad ArvadosApiClient after configuration.
Tom Clegg [Wed, 2 Apr 2014 01:53:13 +0000 (21:53 -0400)]
Load ArvadosApiClient after configuration.

10 years agoMerge branch '2498-group-admin'
Tom Clegg [Wed, 2 Apr 2014 01:35:08 +0000 (21:35 -0400)]
Merge branch '2498-group-admin'

closes #2498

10 years agoFix down-migration: delete the system_group and automatically
Tom Clegg [Wed, 2 Apr 2014 01:27:37 +0000 (21:27 -0400)]
Fix down-migration: delete the system_group and automatically
generated links, and rename the migration.

10 years agoAdd migration to create system group in existing installations.
Tom Clegg [Wed, 2 Apr 2014 00:22:15 +0000 (20:22 -0400)]
Add migration to create system group in existing installations.