arvados.git
9 years agoMerge branch 'master' into 4904-arv-web
Peter Amstutz [Thu, 22 Jan 2015 13:55:14 +0000 (08:55 -0500)]
Merge branch 'master' into 4904-arv-web

9 years agoRevert "4838: Add --set-executable-bit option to make all files from mounted collecti...
Peter Amstutz [Thu, 22 Jan 2015 13:55:01 +0000 (08:55 -0500)]
Revert "4838: Add --set-executable-bit option to make all files from mounted collections be executable."

This reverts commit b97ac7f96234cbbb491bdbaade840ab50802f357.

9 years agoMerge branch '5016-ctrl-c-arv-ws' closes #5016
Peter Amstutz [Wed, 21 Jan 2015 15:51:51 +0000 (10:51 -0500)]
Merge branch '5016-ctrl-c-arv-ws' closes #5016

9 years ago5029: API server uses bugfixed crunch-job.
Brett Smith [Tue, 20 Jan 2015 19:52:29 +0000 (14:52 -0500)]
5029: API server uses bugfixed crunch-job.

Refs #5029.

9 years ago5029: Fix crunch-job logging when SDK requested+virtualenv unavailable.
Brett Smith [Tue, 20 Jan 2015 19:42:48 +0000 (14:42 -0500)]
5029: Fix crunch-job logging when SDK requested+virtualenv unavailable.

* Properly concatenate the message.

* Query and log installed SDK packages in this scenario, since we
  might fall back to what's available in the Docker image.

Closes #5029.

9 years agorefs #4926
Radhika Chippada [Tue, 20 Jan 2015 18:37:04 +0000 (13:37 -0500)]
refs #4926
Merge branch '4926-browser-based-upload'

9 years ago4926: move tutorial_expectations into sections that are describing command line tools.
Radhika Chippada [Tue, 20 Jan 2015 18:35:54 +0000 (13:35 -0500)]
4926: move tutorial_expectations into sections that are describing command line tools.

9 years agoMerge branch '4838-fuse-executable-files' closes #4838
Peter Amstutz [Tue, 20 Jan 2015 17:24:02 +0000 (12:24 -0500)]
Merge branch '4838-fuse-executable-files' closes #4838

9 years ago4838: Set +x on all StreamReaderFiles
Peter Amstutz [Tue, 20 Jan 2015 16:42:54 +0000 (11:42 -0500)]
4838: Set +x on all StreamReaderFiles

9 years ago4926: add description with section links
Radhika Chippada [Mon, 19 Jan 2015 21:42:45 +0000 (16:42 -0500)]
4926: add description with section links

9 years agoMerge branch '4840-workbench-selections-action-forms-wip'
Brett Smith [Mon, 19 Jan 2015 20:27:42 +0000 (15:27 -0500)]
Merge branch '4840-workbench-selections-action-forms-wip'

Closes #4840, #4996.

9 years ago4840: Workbench selection actions are submitted by POST.
Brett Smith [Thu, 15 Jan 2015 22:30:28 +0000 (17:30 -0500)]
4840: Workbench selection actions are submitted by POST.

The previous implementation could get 414 Request URI Too Long
responses by stuffing a large number of selections into the link href.
This commit sidesteps that problem by POSTing the data with a hidden
form instead.  It's based on rails-ujs' strategy for handling links
with data-method that we were already using for some selection
actions, so it should be minimally disruptive.

9 years ago4840: All Workbench selection links toggle dropdown.
Brett Smith [Thu, 15 Jan 2015 22:27:35 +0000 (17:27 -0500)]
4840: All Workbench selection links toggle dropdown.

9 years ago4840: Restore checkbox to project Pipelines and Jobs tab.
Brett Smith [Mon, 5 Jan 2015 20:43:50 +0000 (15:43 -0500)]
4840: Restore checkbox to project Pipelines and Jobs tab.

9 years agoMerge branch 'master' into 4926-browser-based-upload
Radhika Chippada [Mon, 19 Jan 2015 19:35:54 +0000 (14:35 -0500)]
Merge branch 'master' into 4926-browser-based-upload

9 years ago4904: Inspect event type and only print collection create events.
Peter Amstutz [Mon, 19 Jan 2015 16:28:02 +0000 (11:28 -0500)]
4904: Inspect event type and only print collection create events.

9 years ago4904: Minimal event subscribe example.
Peter Amstutz [Mon, 19 Jan 2015 15:01:41 +0000 (10:01 -0500)]
4904: Minimal event subscribe example.

9 years ago5016: PollClient.run_forever() polls self.stop() in order to have a chance to process...
Peter Amstutz [Mon, 19 Jan 2015 14:49:43 +0000 (09:49 -0500)]
5016: PollClient.run_forever() polls self.stop() in order to have a chance to process KeyboardInterrupt.

9 years ago4904: Added docker_image files to samples. Added discussion about using your
Peter Amstutz [Mon, 19 Jan 2015 14:20:08 +0000 (09:20 -0500)]
4904: Added docker_image files to samples.  Added discussion about using your
own docker image, and about benefits of immutable applications.

9 years ago4904: Fix markup of links for phusion passenger and apache, and add links to WSGI...
Peter Amstutz [Mon, 19 Jan 2015 13:52:11 +0000 (08:52 -0500)]
4904: Fix markup of links for phusion passenger and apache, and add links to WSGI and Rack.

9 years agocloses #3686
Radhika Chippada [Fri, 16 Jan 2015 23:20:07 +0000 (18:20 -0500)]
closes #3686
Merge branch '3686-sharing-repositories'

9 years ago3686: ensure Advanced is always the last pane even after adding the Sharing pane.
Radhika Chippada [Fri, 16 Jan 2015 23:18:22 +0000 (18:18 -0500)]
3686: ensure Advanced is always the last pane even after adding the Sharing pane.

9 years ago4904: Moved to services/, finished first draft documentation.
Peter Amstutz [Fri, 16 Jan 2015 21:57:49 +0000 (16:57 -0500)]
4904: Moved to services/, finished first draft documentation.

9 years agoMerge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Fri, 16 Jan 2015 21:06:12 +0000 (16:06 -0500)]
Merge branch 'master' into 3686-sharing-repositories

9 years agoMerge branch '4922-google-api-client-force-install'
Tim Pierce [Fri, 16 Jan 2015 20:50:32 +0000 (15:50 -0500)]
Merge branch '4922-google-api-client-force-install'

Fixes #4922.

9 years ago4922: force google-api-python-client install
Tim Pierce [Fri, 16 Jan 2015 19:51:28 +0000 (14:51 -0500)]
4922: force google-api-python-client install

Install google-api-python-client with 'pip install -I' to fix the case
where the Docker image already has an older version of
google-api-python-client installed.

9 years agoAdd 'apps/arv-web/' from commit 'f9732ad8460d013c2f28363655d0d1b91894dca5'
Peter Amstutz [Fri, 16 Jan 2015 19:05:48 +0000 (14:05 -0500)]
Add 'apps/arv-web/' from commit 'f9732ad8460d013c2f28363655d0d1b91894dca5'

git-subtree-dir: apps/arv-web
git-subtree-mainline: b97ac7f96234cbbb491bdbaade840ab50802f357
git-subtree-split: f9732ad8460d013c2f28363655d0d1b91894dca5

9 years ago4904: Rename to arv-web.py to reflect a more general purpose tool.
Peter Amstutz [Fri, 16 Jan 2015 19:05:33 +0000 (14:05 -0500)]
4904: Rename to arv-web.py to reflect a more general purpose tool.

9 years ago4904: CGI sample works.
Peter Amstutz [Fri, 16 Jan 2015 18:54:42 +0000 (13:54 -0500)]
4904: CGI sample works.

9 years ago4838: Add --set-executable-bit option to make all files from mounted collections...
Peter Amstutz [Fri, 16 Jan 2015 18:30:13 +0000 (13:30 -0500)]
4838: Add --set-executable-bit option to make all files from mounted collections be executable.

9 years agoUpdate bundle. refs #3021
Tom Clegg [Fri, 16 Jan 2015 17:26:17 +0000 (12:26 -0500)]
Update bundle. refs #3021

9 years agoConfigure dockerfile with passenger. Add sample applications.
Peter Amstutz [Fri, 16 Jan 2015 17:02:55 +0000 (12:02 -0500)]
Configure dockerfile with passenger.  Add sample applications.

9 years agoMerge branch '3021-workbench-perf' refs #3021
Tom Clegg [Fri, 16 Jan 2015 06:37:58 +0000 (01:37 -0500)]
Merge branch '3021-workbench-perf' refs #3021

9 years ago3021: Reset API fixtures before running the first test case.
Tom Clegg [Fri, 16 Jan 2015 03:22:26 +0000 (22:22 -0500)]
3021: Reset API fixtures before running the first test case.

9 years ago3021: Do not drop/create API database at startup if run-tests.sh has done that for us.
Tom Clegg [Fri, 16 Jan 2015 01:24:11 +0000 (20:24 -0500)]
3021: Do not drop/create API database at startup if run-tests.sh has done that for us.

9 years ago3021: Revert "3021: Do not drop/create API database at startup: run-tests.sh does...
Tom Clegg [Fri, 16 Jan 2015 01:22:19 +0000 (20:22 -0500)]
3021: Revert "3021: Do not drop/create API database at startup: run-tests.sh does that for us."

This reverts commit 591446b97754292031a4214f08039adebd56cfe8.

9 years ago3021: Merge branch 'master' into 3021-workbench-perf
Tom Clegg [Thu, 15 Jan 2015 21:29:59 +0000 (16:29 -0500)]
3021: Merge branch 'master' into 3021-workbench-perf

9 years ago3021: Do not show user notifications on error pages.
Tom Clegg [Thu, 15 Jan 2015 17:50:11 +0000 (12:50 -0500)]
3021: Do not show user notifications on error pages.

9 years ago3021: Update Gemfile for Ruby SDK bugfix.
Tom Clegg [Thu, 15 Jan 2015 17:42:59 +0000 (12:42 -0500)]
3021: Update Gemfile for Ruby SDK bugfix.

9 years agoMerge branch '3835-pysdk-keep-exceptions-wip'
Brett Smith [Thu, 15 Jan 2015 17:00:13 +0000 (12:00 -0500)]
Merge branch '3835-pysdk-keep-exceptions-wip'

Closes #3835, #4972.

9 years ago3021: Remove reference to deleted speclist arg.
Tom Clegg [Thu, 15 Jan 2015 16:59:20 +0000 (11:59 -0500)]
3021: Remove reference to deleted speclist arg.

9 years ago3835: PySDK raises NotFoundError when all Keep services report such.
Brett Smith [Wed, 14 Jan 2015 20:22:24 +0000 (15:22 -0500)]
3835: PySDK raises NotFoundError when all Keep services report such.

Previously, we raised this error when >= 75% of services reported
such, as the most reasonable available cutoff to make the
distinction.  Now that Keep exceptions include detailed information
about the error from each service, it seems useful to make this
threshold stricter, and only raise NotFoundError when we're sure
that's the problem.  See further discussion from
<https://arvados.org/issues/3835#note-11>.

9 years ago3835: Improve error reporting in PySDK Keep client.
Brett Smith [Fri, 9 Jan 2015 18:15:07 +0000 (13:15 -0500)]
3835: Improve error reporting in PySDK Keep client.

* Create a KeepRequestError base exception to store information about
  errors encountered when talking to Keep services, and include those
  in the default formatting.
* Include Keep service error information in exceptions raised by the
  Keep client.

9 years agoMerge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Thu, 15 Jan 2015 16:13:27 +0000 (11:13 -0500)]
Merge branch 'master' into 3686-sharing-repositories

9 years ago4926: trailing white space
Radhika Chippada [Thu, 15 Jan 2015 16:02:41 +0000 (11:02 -0500)]
4926: trailing white space

9 years agoMerge branch 'master' into 4926-browser-based-upload
Radhika Chippada [Thu, 15 Jan 2015 16:00:25 +0000 (11:00 -0500)]
Merge branch 'master' into 4926-browser-based-upload

9 years ago4926: minor text update
Radhika Chippada [Thu, 15 Jan 2015 15:59:56 +0000 (10:59 -0500)]
4926: minor text update

9 years agoReduce file_names limit to 2^12. refs #4523.
Tom Clegg [Wed, 14 Jan 2015 22:33:18 +0000 (17:33 -0500)]
Reduce file_names limit to 2^12. refs #4523.

9 years ago4904: Renamed "runit.py" to "arv-web-example.py"
Peter Amstutz [Wed, 14 Jan 2015 21:21:52 +0000 (16:21 -0500)]
4904: Renamed "runit.py" to "arv-web-example.py"

9 years ago4926: improved image quality
Radhika Chippada [Wed, 14 Jan 2015 21:21:22 +0000 (16:21 -0500)]
4926: improved image quality

9 years ago4904: Fixed event listening. Terminates properly on signals. Tested and works now.
Peter Amstutz [Wed, 14 Jan 2015 21:14:05 +0000 (16:14 -0500)]
4904: Fixed event listening.  Terminates properly on signals.  Tested and works now.

9 years agoMerge branch 'master' into 4926-browser-based-upload
Radhika Chippada [Wed, 14 Jan 2015 20:41:25 +0000 (15:41 -0500)]
Merge branch 'master' into 4926-browser-based-upload

9 years agocloses #4523
Radhika Chippada [Wed, 14 Jan 2015 20:34:50 +0000 (15:34 -0500)]
closes #4523
Merge branch '4523-search-index'

9 years ago4926: download images
Radhika Chippada [Wed, 14 Jan 2015 20:33:19 +0000 (15:33 -0500)]
4926: download images

9 years ago4926: expand downloading data section
Radhika Chippada [Wed, 14 Jan 2015 20:32:10 +0000 (15:32 -0500)]
4926: expand downloading data section

9 years ago4904: Chooses most recently modified collection and runs web service on it.
Peter Amstutz [Wed, 14 Jan 2015 20:21:04 +0000 (15:21 -0500)]
4904: Chooses most recently modified collection and runs web service on it.

9 years agoMerge branch '4523-search-index-TC' into 4523-search-index
Radhika Chippada [Wed, 14 Jan 2015 20:21:03 +0000 (15:21 -0500)]
Merge branch '4523-search-index-TC' into 4523-search-index

Conflicts:
services/api/test/integration/collections_api_test.rb

9 years ago4904: Set up fuse, set up event bus, run docker
Peter Amstutz [Wed, 14 Jan 2015 19:59:37 +0000 (14:59 -0500)]
4904: Set up fuse, set up event bus, run docker

9 years ago4523: Clear up manifest-signing vs. locator-signing.
Tom Clegg [Wed, 14 Jan 2015 19:41:39 +0000 (14:41 -0500)]
4523: Clear up manifest-signing vs. locator-signing.

9 years ago4523: update signed_locator in test
Radhika Chippada [Wed, 14 Jan 2015 19:14:38 +0000 (14:14 -0500)]
4523: update signed_locator in test

9 years agoMerge branch 'master' into 4926-browser-based-upload
Radhika Chippada [Wed, 14 Jan 2015 18:38:45 +0000 (13:38 -0500)]
Merge branch 'master' into 4926-browser-based-upload

9 years agoMerge branch 'master' into 4523-search-index
Radhika Chippada [Wed, 14 Jan 2015 18:12:22 +0000 (13:12 -0500)]
Merge branch 'master' into 4523-search-index

9 years ago4523: try to resolve column order by down and up migrations through VERSION=201408170...
Radhika Chippada [Wed, 14 Jan 2015 18:11:03 +0000 (13:11 -0500)]
4523: try to resolve column order by down and up migrations through VERSION=20140817035914

9 years ago4523: use filters instead of where for search
Radhika Chippada [Wed, 14 Jan 2015 18:06:21 +0000 (13:06 -0500)]
4523: use filters instead of where for search

9 years ago4523: check for a specific file name and stream names in file_names.
Radhika Chippada [Wed, 14 Jan 2015 17:54:41 +0000 (12:54 -0500)]
4523: check for a specific file name and stream names in file_names.

9 years agoPython packages use python-daemon<2.
Brett Smith [Wed, 14 Jan 2015 17:47:38 +0000 (12:47 -0500)]
Python packages use python-daemon<2.

It's good to see python-daemon under active development, but they're
working out so many little issues so rapidly that we're having a hard
time keeping on top of them in our builds.  We're pinning the version
until things settle down a little.  No issue #.

9 years ago4523: update migration script to use execute instead of update_sql so that output...
Radhika Chippada [Wed, 14 Jan 2015 16:24:20 +0000 (11:24 -0500)]
4523: update migration script to use execute instead of update_sql so that output is not printed to console.

9 years agoMerge branch 'master' into 4523-search-index
Radhika Chippada [Wed, 14 Jan 2015 16:15:33 +0000 (11:15 -0500)]
Merge branch 'master' into 4523-search-index

9 years agocloses #3756
Radhika Chippada [Wed, 14 Jan 2015 16:14:56 +0000 (11:14 -0500)]
closes #3756
Merge branch '3756-show-user-button'

9 years agoMerge branch 'master' into 3756-show-user-button
Radhika Chippada [Wed, 14 Jan 2015 16:13:49 +0000 (11:13 -0500)]
Merge branch 'master' into 3756-show-user-button

9 years agoMerge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Wed, 14 Jan 2015 16:12:47 +0000 (11:12 -0500)]
Merge branch 'master' into 3686-sharing-repositories

9 years ago3686: Support sharing pane in repository show page.
Radhika Chippada [Wed, 14 Jan 2015 16:10:27 +0000 (11:10 -0500)]
3686: Support sharing pane in repository show page.
Refactor current project sharing work into application area and reuse it for sharing repositories.
Refactor methods used by tests into helper and reuse in repository sharing tests.

9 years ago3021: Merge branch 'master' into 3021-workbench-perf
Tom Clegg [Tue, 13 Jan 2015 21:49:50 +0000 (16:49 -0500)]
3021: Merge branch 'master' into 3021-workbench-perf

9 years agoMerge branch '4968-refresh-project-dir' closes #4968
Peter Amstutz [Tue, 13 Jan 2015 20:15:56 +0000 (15:15 -0500)]
Merge branch '4968-refresh-project-dir' closes #4968

9 years ago4523: update migrate script to use batch size and instance method on collection.
Radhika Chippada [Tue, 13 Jan 2015 18:39:29 +0000 (13:39 -0500)]
4523: update migrate script to use batch size and instance method on collection.

9 years agoMerge branch 'master' into 4523-search-index
Radhika Chippada [Tue, 13 Jan 2015 17:03:56 +0000 (12:03 -0500)]
Merge branch 'master' into 4523-search-index

9 years ago3021: Do not check user notifications unless they are going to be displayed.
Tom Clegg [Tue, 13 Jan 2015 15:33:53 +0000 (10:33 -0500)]
3021: Do not check user notifications unless they are going to be displayed.

9 years ago3021: Add web-inspectable profiling mode.
Tom Clegg [Tue, 13 Jan 2015 15:18:16 +0000 (10:18 -0500)]
3021: Add web-inspectable profiling mode.

* Run Workbench with environment variable ENABLE_PROFILING=yes. Timing
  figures should appear at the top left of each page. Click to get
  more detail.

* Visit {workbench-uri}?pp=flamegraph to see a profiling graph instead
  of the requested page itself.

* More: https://github.com/MiniProfiler/rack-mini-profiler

9 years agoExplicitly specify ruby 2.1 in "rvm alias" no issue #
Peter Amstutz [Mon, 12 Jan 2015 21:56:09 +0000 (16:56 -0500)]
Explicitly specify ruby 2.1 in "rvm alias" no issue #

9 years ago4968: Fix polling refresh on project directories
Peter Amstutz [Fri, 9 Jan 2015 02:26:32 +0000 (21:26 -0500)]
4968: Fix polling refresh on project directories

9 years ago3756: do not show 'Show' button in admin user's own row.
Radhika Chippada [Mon, 12 Jan 2015 19:01:40 +0000 (14:01 -0500)]
3756: do not show 'Show' button in admin user's own row.

9 years agoMerge branch '4924-arv-edit-error-handling' closes #4924
Peter Amstutz [Mon, 12 Jan 2015 18:39:34 +0000 (13:39 -0500)]
Merge branch '4924-arv-edit-error-handling' closes #4924

9 years ago4924: Collapse JSON rescue blocks to reduce duplicate code.
Peter Amstutz [Mon, 12 Jan 2015 18:38:45 +0000 (13:38 -0500)]
4924: Collapse JSON rescue blocks to reduce duplicate code.

9 years ago4924: Update prints uuid from results, not the uuid originally specified.
Peter Amstutz [Mon, 12 Jan 2015 17:23:40 +0000 (12:23 -0500)]
4924: Update prints uuid from results, not the uuid originally specified.
Catch Oj::ParseError as well as JSON::ParserError.  Titleize only HTTP status
messages, not every error message.

9 years ago4924: Rename HTTPResponse to ArvadosAPIError. Use NET::HTTP Response titles
Peter Amstutz [Mon, 12 Jan 2015 15:33:36 +0000 (10:33 -0500)]
4924: Rename HTTPResponse to ArvadosAPIError.  Use NET::HTTP Response titles
for error codes if no other error is available.

9 years ago3021: Optimize manifest parsing.
Tom Clegg [Sun, 11 Jan 2015 19:55:21 +0000 (14:55 -0500)]
3021: Optimize manifest parsing.

9 years ago3021: Update bundle.
Tom Clegg [Sun, 11 Jan 2015 08:01:26 +0000 (03:01 -0500)]
3021: Update bundle.

9 years ago3021: Do not drop/create API database at startup: run-tests.sh does that for us.
Tom Clegg [Sun, 11 Jan 2015 07:36:35 +0000 (02:36 -0500)]
3021: Do not drop/create API database at startup: run-tests.sh does that for us.

9 years ago3021: Fix races in performance test.
Tom Clegg [Sun, 11 Jan 2015 07:35:29 +0000 (02:35 -0500)]
3021: Fix races in performance test.

9 years ago4523: revert test update now that text attributes in non-collections objects are...
Radhika Chippada [Sat, 10 Jan 2015 02:28:04 +0000 (21:28 -0500)]
4523: revert test update now that text attributes in non-collections objects are not omitted from search index.

9 years agoMerge branch 'master' into 4523-search-index
Radhika Chippada [Sat, 10 Jan 2015 02:07:06 +0000 (21:07 -0500)]
Merge branch 'master' into 4523-search-index

9 years ago4523: include stream names in file_names
Radhika Chippada [Fri, 9 Jan 2015 23:11:10 +0000 (18:11 -0500)]
4523: include stream names in file_names

9 years ago4523: exclude manifest_text from collection -> searchable_columns and leave the other...
Radhika Chippada [Fri, 9 Jan 2015 23:00:07 +0000 (18:00 -0500)]
4523: exclude manifest_text from collection -> searchable_columns and leave the other text columns for other objects.

9 years agoAdd a magic pseudoclass to body, instead of appending a magic div. Selenium seems...
Tom Clegg [Fri, 9 Jan 2015 22:46:15 +0000 (17:46 -0500)]
Add a magic pseudoclass to body, instead of appending a magic div. Selenium seems to like this better. refs #3021

9 years agoDiagnostics really do need selenium. refs #3021
Tom Clegg [Fri, 9 Jan 2015 22:45:23 +0000 (17:45 -0500)]
Diagnostics really do need selenium. refs #3021

9 years agoMake angular shim minify-safe. No issue #
Tom Clegg [Fri, 9 Jan 2015 22:09:28 +0000 (17:09 -0500)]
Make angular shim minify-safe. No issue #

9 years agoMerge branch 'master' into 4523-search-index
Radhika Chippada [Fri, 9 Jan 2015 21:49:36 +0000 (16:49 -0500)]
Merge branch 'master' into 4523-search-index

9 years ago4926: add "upload using workbench"
Radhika Chippada [Fri, 9 Jan 2015 21:43:35 +0000 (16:43 -0500)]
4926: add "upload using workbench"

9 years ago4924: Distinguish between errors the user can do something about (syntax errors
Peter Amstutz [Fri, 9 Jan 2015 20:37:42 +0000 (15:37 -0500)]
4924: Distinguish between errors the user can do something about (syntax errors
or well-formed server errors) and errors that the user probably can't recover
from (everything else.)  Prints "Updated object" on success.

9 years ago4523: update migration script to use sql to set file_names
Radhika Chippada [Fri, 9 Jan 2015 02:51:14 +0000 (21:51 -0500)]
4523: update migration script to use sql to set file_names