Arvados

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2440

Review 2228-check-filter-uuid-columns

Tom Clegg

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2271

Review 2107-radhika-user-guide-minor-updates branch for Radhika

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2325

2221-complete-docker code review

Tim Pierce

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2596 2596 Tom Clegg Tom Clegg 3 Workbench mangles script_parameters when starting a pipeline_instance Resolved Resolved 3 1.0 1.0 1.0 2596 36 3 61 1 1.0	2597 2597 Fix handling of script_parameters when creating/editing a pipeline instance Tom Clegg 3 0 2596 3 36 -c-a 5 2598 2598 Write tests for pipeline instance #create and #update Tom Clegg 3 0 2596 3 36 -c-a 5 2605 2605 Review 2596-refactor-pipeline-create branch Tom Clegg 3 0 2596 3 36 -c-a 5
2461 2461 Brett Smith Brett Smith 79 Specify design for Crunch v2 Resolved Resolved 3 1.0 1.0 1.0 2461 36 79 61 6 1.0	2578 2578 Organize meeting to finalize Crunch v2 design Should definitely include Tom. Other people may attend as desired. Can happen during merge week. Brett Smith 79 0 2461 3 36 -c-a 5
1968 1968 Misha Zatsman Misha Zatsman 82 Monitor disk usage (per user and per site; split by transient/persistent; optionally weighted by #users who want persistent). Closed Closed 5 2.0 2.0 2.0 1968 36 82 61 6 2.0	2572 2572 Report weighted disk usage based on users' desired replication. simple formula: the cost for the nth copy is split evenly by all the users who want at least n copies of the data. Misha Zatsman 82 0 1968 3 36 -c-a 5 2571 2571 Read (and store) replication preferences from "want" link properties. Misha Zatsman 82 0 1968 3 36 -c-a 5 2590 2590 Report deletion candidates sorted by age. Misha Zatsman 82 0 1968 3 36 -c-a 5 2574 2574 Report blocks that are replicated less than the max desired by all persisters. Misha Zatsman 82 0 1968 3 36 -c-a 5 2579 2579 Starting logging to the API server, Misha Zatsman 82 0 1968 3 36 -c-a 5 2573 2573 Modify reader disk usage numbers to not consider disk replication. Misha Zatsman 82 0 1968 3 36 -c-a 5 1757 1757 User can see in Workbench total amount storage space being used 0 1968 3 36 -c-a 5
2282 2282 Tim Pierce Tim Pierce 44 Recurring: write blog post about latest release. Resolved Resolved 3 1.0 1.0 1.0 2282 36 44 61 6 1.0		2289 2289 Write release summary. Tim Pierce 44 0 2282 5 36 -c-a 5
2451 2451 Tom Clegg Tom Clegg 3 Developer documentation for Workbench Resolved Resolved 3 1.0 1.0 1.0 2451 36 3 61 6 1.0	2471 2471 Write "Hacking Workbench" wiki page Tom Clegg 3 0 2451 3 36 -c-a 5 2495 2495 Fill in detail for more dev tasks ajax stuff Tom Clegg 3 0 2451 3 36 -c-a 5
2376 2376 Peter Amstutz Peter Amstutz 47 Workbench should display collection tags everywhere it shows collection UUIDs Resolved Resolved 3 3.0 3.0 3.0 2376 36 47 61 2 3.0	2602 2602 Review 2376 Peter Amstutz 47 0 2376 3 36 -c-a 5 2465 2465 Use standard functions to render UUID text/links anywhere that isn't already being used. Peter Amstutz 47 0 2376 3 36 -c-a 5 2467 2467 Make standard UUID labels include tags Peter Amstutz 47 0 2376 3 36 -c-a 5
2484 2484 Peter Amstutz Peter Amstutz 47 Workbench error when combining existing collections to make a new collection (encountered by Jonathan 2014-03-26) Resolved Resolved 3 0.5 0.5 0.5 2484 36 47 61 1 0.5
2450 2450 Peter Amstutz Peter Amstutz 47 Metadata server prototype demonstrates permissions and results reported to the team Resolved Resolved 3 5.0 5.0 5.0 2450 36 47 61 6 5.0	2458 2458 Import from Postgres Peter Amstutz 47 0 2450 3 36 -c-a 5 2459 2459 Prototype permissions Peter Amstutz 47 0 2450 3 36 -c-a 5 2457 2457 Set up BigData SPARQL server Peter Amstutz 47 0 2450 3 36 -c-a 5
2488 2488 Peter Amstutz Peter Amstutz 47 Update http://doc.arvados.org/api/schema/Job.html re. nondeterministic and repository attributes Resolved Resolved 3 1.0 1.0 1.0 2488 36 47 61 1 1.0	2577 2577 Copy text from pipeline documentation Peter Amstutz 47 0 2488 3 36 -c-a 5 2594 2594 Review 2488-jobs-pipeline-doc Peter Amstutz 47 0 2488 3 36 -c-a 5
2582 2582 Ward Vandewege Ward Vandewege 1 shell nodes should have 80/443 open by default Resolved Resolved 3 1.0 1.0 1.0 2582 36 1 61 2 1.0	2585 2585 ask misha to run his code on his shell node rather than qr1hi Ward Vandewege 1 0 2582 3 36 -c-a 5 2583 2583 update shell node creation procedure docs accordingly Ward Vandewege 1 0 2582 3 36 -c-a 5 2584 2584 open 80/443 to all existing (qr1hi) shell nodes Ward Vandewege 1 0 2582 3 36 -c-a 5
2388 2388 Tom Clegg Tom Clegg 3 Reload on login screen failed Resolved Resolved 3 1.0 1.0 1.0 2388 36 3 61 1 1.0	2600 2600 Review 2388-bogus-token-error-page Tom Clegg 3 0 2388 3 36 -c-a 5 2599 2599 Add tests to expose crash condition Tom Clegg 3 0 2388 3 36 -c-a 5 2575 2575 DTRT when a user presents a valid token pointing to a non-existent user Tom Clegg 3 0 2388 3 36 -c-a 5
2449 2449 Tim Pierce Tim Pierce 44 New Keep server can write Resolved Resolved 3 5.0 5.0 5.0 2449 36 44 61 1 5.0		2463 2463 Keep: command-line flags desirable command-line options for Keep to support: * @--port@ - TCP port to listen on (default 25107) * @--ssl@ - enable SSL (default: ??) * @--volume=@ - specify directory to a Keep volume * @--max-connections=@ - maximum number of concurrent connections to accept * other options existing in Warehouse Tim Pierce 44 2.0 2449 5 36 -c-a 5 2561 2561 Keep: /index and /status handlers * GET /index.txt → one line per block stored on disk: hash+size <space> modtime_unix_timestamp * GET /status.json → a json document something like this <pre><code class="javascript"> { "volumes":[ {"mount_point":"/data/disk0","bytes_free":4882337792,"bytes_used":5149708288}, {"mount_point":"/data/disk1","bytes_free":39614472192,"bytes_used":3314229248} ] } </code></pre> Tim Pierce 44 4.0 2449 5 36 -c-a 5 2603 2603 Review 2449-keep-index-status-handlers Tim Pierce 44 0 2449 5 36 -c-a 5 2507 2507 Review 2449-keep-write-blocks Code review for 2449-keep-write-blocks: https://arvados.org/projects/arvados/repository/diff?utf8=%E2%9C%93&rev=f6b24b30e9f3794943f628c22ee4dabcadca5a1a&rev_to=ad0944aa970bf52bcc2387ac57e12cb69ae54d66 Tim Pierce 44 0 2449 5 36 -c-a 5 2292 2292 Keep server writes Warehouse blocks Tim Pierce 44 16.0 2449 5 36 -c-a 5 2591 2591 Review 2449-keep-flags Review for issue #2463: add command line flags support to Keep This branch adds @-listen@ and @-volume@ flags to Keep: * @-listen@ specifies the interface on which to listen for requests. Examples: @-listen=127.0.0.1:4949@ @-listen=:25107@ (listen on port 25107 on all interfaces) * @-volumes@ specifies a list of directories to use as keep volumes. Example: @-volumes=/var/keep01,/var/keep02,/var/keep03/subdir@ If @-volumes@ is empty or is not present, Keep will select volumes by looking at currently mounted filesystems for @/keep@ top-level directories. git diff master...2449-keep-flags Misha Zatsman 82 0 2449 5 36 -c-a 5 2460 2460 Keep: unit tests for writing blocks Tim Pierce 44 8.0 2449 5 36 -c-a 5
2217 2217 Ward Vandewege Ward Vandewege 1 Puppetize script that records VM logins Resolved Resolved 3 1.0 1.0 1.0 2217 36 1 61 2 1.0	2446 2446 puppetize login script Ward Vandewege 1 0 2217 3 36 -c-a 5 2444 2444 re-enable login script on qr1hi 0 2217 3 36 -c-a 5
1776 1776 Radhika Chippada Radhika Chippada 72 User receives automatic email notification when account gets activated Resolved Resolved 3 1.0 1.0 1.0 1776 36 72 61 6 1.0	2558 2558 Add send_notification_email optional parameter to the setup-new-user script and send it when invoking setup method Radhika Chippada 72 0 1776 3 36 -c-a 5 2557 2557 Add send_notification_email config param to workbench and send it during the setup method invocations Radhika Chippada 72 0 1776 3 36 -c-a 5 2556 2556 Test mailer functionality Radhika Chippada 72 0 1776 3 36 -c-a 5 2555 2555 Update users.setup to send email on success Radhika Chippada 72 0 1776 3 36 -c-a 5 2554 2554 Add mailer named UserNotifier Add mailer, model, and view. Radhika Chippada 72 0 1776 3 36 -c-a 5 2586 2586 Add theme to api server similar to workbench Radhika Chippada 72 0 1776 3 36 -c-a 5 2581 2581 Review 1776 implementation Radhika Chippada 72 0 1776 3 36 -c-a 5
2375 2375 Brett Smith Brett Smith 79 Add a row to the Logs table whenever a row in any other [interesting] table is created or changed Resolved Resolved 3 1.0 1.0 1.0 2375 36 79 61 2 1.0	2469 2469 alter existing logs table to support logging of changes Brett Smith 79 0 2375 3 36 -c-a 5 2468 2468 write one little code section (rake middleware? strategically placed active record call? Cf. acts-as-versioned gem) to log changes Brett Smith 79 0 2375 3 36 -c-a 5 2559 2559 Review 2375-log-table Brett Smith 79 0 2375 3 36 -c-a 5
2228 2228 Peter Amstutz Peter Amstutz 47 In create and update, assign/check _kind attributes by inspecting corresponding _uuid. Resolved Resolved 3 1.0 1.0 1.0 2228 36 47 61 2 1.0	2304 2304 Reject create/update if _uuid is an arvados object but does not map to a real object that is visible to the current user Peter Amstutz 47 0 2228 3 36 -c-a 5 2418 2418 Add "is_a" to filters Peter Amstutz 47 0 2228 3 36 -c-a 5 2436 2436 Remove _kind columns Peter Amstutz 47 0 2228 3 36 -c-a 5 2303 2303 Remove now-unnecessary _kind values in tutorials/docs/examples Peter Amstutz 47 0 2228 3 36 -c-a 5 2417 2417 Write tests Peter Amstutz 47 0 2228 3 36 -c-a 5 2311 2311 Check that owner_uuid exists (even though it has no corresponding _kind) Peter Amstutz 47 0 2228 3 36 -c-a 5	2298 2298 Reject mismatched _kind/_uuid pairs in before_create/update hooks in ArvadosModel Peter Amstutz 47 0 2228 5 36 -c-a 5 2299 2299 Fill in _type automatically if not provided and corresponding _uuid is provided Peter Amstutz 47 0 2228 5 36 -c-a 5
2246 2246 Tom Clegg Tom Clegg 3 Race condition in crunch-job: multiple jobs use the same /tmp/crunch-job/ on head node to check out git trees and make archives. Fix as simple as using git archive --remote? Resolved Resolved 3 1.0 1.0 1.0 2246 36 3 61 1 1.0	2521 2521 Use git in --remote mode instead of checking out repository on head node Tom Clegg 3 0 2246 3 36 -c-a 5 2564 2564 Review 2246-fix-git-clone-race Tom Clegg 3 0 2246 3 36 -c-a 5
2547 2547 keep0 and keep1.qr1hi each report 2x most blocks. Resolved Resolved 3 0.5 0.5 0.5 2547 36 61 1 0.5	2567 2567 Figure out why, and fix Tom Clegg 3 0 2547 3 36 -c-a 5
2487 2487 Tim Pierce Tim Pierce 44 Finish/merge last sprint's docker work. Resolved Resolved 3 1.0 1.0 1.0 2487 36 44 61 2 1.0
2107 2107 Brett Smith Brett Smith 79 Documentation 50 Documentation Recurring: ensure docs/tutorials are up-to-date with latest release. Resolved Resolved 3 1.0 1.0 1.0 2107 36 79 61 6 1.0	2268 2268 2107-radhika-user-guide-minor-updates is good to be merged, with one small change (see description) You introduce a space at the end of a line in this file: doc/user/tutorials/tutorial-firstscript.html.textile.liquid If you fix that, I think you can merge this branch into master. Radhika Chippada 72 0 2107 3 36 -c-a 5 2136 2136 Update docs for 2014-03-26 sprint Brett Smith 79 0 2107 3 36 -c-a 5 2470 2470 Update docs for 2014-04-16 sprint Brett Smith 79 0 2107 3 36 -c-a 5 2490 2490 Review 2470-doc-refresh Brett Smith 79 0 2107 3 36 -c-a 5
2338 2338 Tom Clegg Tom Clegg 3 Pipeline instance reloads interfere with user's tab selection Resolved Resolved 3 1.0 1.0 1.0 2338 36 3 61 1 1.0	2520 2520 Stash and restore current tab selection when replacing body content in js view Tom Clegg 3 0 2338 3 36 -c-a 5 2563 2563 Review 2338-maintain-active-tab Tom Clegg 3 0 2338 3 36 -c-a 5
2243 2243 Tom Clegg Tom Clegg 3 Pipeline instance page H2 should be the instance's name, not the template's name. Resolved Resolved 3 1.0 1.0 1.0 2243 36 3 61 1 1.0	2497 2497 Show instance name on instance#show, with template name as subheading/link. Tom Clegg 3 0 2243 3 36 -c-a 5 2562 2562 Review 2243-fix-pipeline-instance-heading Tom Clegg 3 0 2243 3 36 -c-a 5
2272 2272 Radhika Chippada Radhika Chippada 72 Admin can run setup-new-user.rb equivalent with a nice form from workbench Resolved Resolved 3 1.0 1.0 1.0 2272 36 72 61 2 1.0	2516 2516 Learn how to use bootstrap modal to display a popup modal during setup. Radhika Chippada 72 8.0 2272 3 36 -c-a 5 2515 2515 Update the "Add a new user" button to use the setup action Reuse the setup popup to add a new user. Radhika Chippada 72 8.0 2272 3 36 -c-a 5 2514 2514 Add a "setup" link in the User -> Admin tab in the Workbench UI - Use bootstrap modal to prompt for input parameters. - Add a workbench controller action for setup Radhika Chippada 72 12.0 2272 3 36 -c-a 5 2513 2513 Functional tests using Capybara 1 day to learn to use Capybara 1 to 2 days to write the tests. Radhika Chippada 72 20.0 2272 3 36 -c-a 5 2517 2517 Review implemenation Tom Clegg 3 0 2272 3 36 -c-a 5
2508 2508 Tom Clegg Tom Clegg 3 Sasha gets "fiddlesticks" error when logging in to qr1hi. Rejected Rejected 6 1.0 1.0 1.0 2508 36 3 61 1 1.0	2519 2519 Reproduce bug Tom Clegg 3 0 2508 3 36 -c-a 5
2509 2509 Ward Vandewege Ward Vandewege 1 doc: make rake linkchecker task and describe in readme Resolved Resolved 3 0.5 0.5 0.5 2509 36 1 61 2 0.5	2512 2512 update run-tests.sh on ci to use rake linkchecker Ward Vandewege 1 0 2509 3 36 -c-a 5 2510 2510 Review 2509-rake-linkchecker Ward Vandewege 1 0 2509 3 36 -c-a 5 2511 2511 add rake linkchecker + update docs Ward Vandewege 1 0 2509 3 36 -c-a 5
2209 2209 arvados.api('v1').collections().list(limit=X).execute() returns ~half X results Resolved Resolved 3 1.0 1.0 1.0 2209 36 61 1 1.0	2491 2491 Reproduce "available > returned < limit" and write test Tom Clegg 3 0 2209 3 36 -c-a 5 2410 2410 Merge 2209 branch (it just adds some tests) Tom Clegg 3 0 2209 3 36 -c-a 5 2493 2493 Fix inaccurate items_available current user has permission to collection via multiple groups/links. Tom Clegg 3 0 2209 3 36 -c-a 5 2494 2494 Review 2209-correct-items-available branch Tom Clegg 3 0 2209 3 36 -c-a 5	2373 2373 Figure out why, and fix. Start with paging branch. Tom Clegg 3 0 2209 5 36 -c-a 5
2447 2447 Tom Clegg Tom Clegg 3 Workbench search is broken - it always returns everything Resolved Resolved 3 1.0 1.0 1.0 2447 36 3 61 1 1.0	2496 2496 Figure out why, and fix it. Tom Clegg 3 0 2447 3 36 -c-a 5 2506 2506 Review 2447-fix-workbench-search branch. I note searching for owner_uuid is explicitly disallowed. Should there be similar restrictions on the links table? As in, presumably we probably don't want the links table searchable? Not sure why b0542ec0dd2bb6fbf040d1c7d719e7fa4d82d58a is in this branch but it seems to make sense too. Good to merge, I think. Ward Vandewege 1 0 2447 3 36 -c-a 5
2498 2498 Support finer grained administrator permissions like read-only, only certain users. Resolved Resolved 3 1.0 1.0 1.0 2498 36 61 2 1.0	2499 2499 Modify permission mechanism, add tests, update docs. Tom Clegg 3 0 2498 3 36 -c-a 5 2500 2500 Review 2498-group-admin branch Just one suggested change: the down migration should wipe the group, I think... That's the expected behavior for migrations. Otherwise, good to merge. Ward Vandewege 1 0 2498 3 36 -c-a 5
2068 2068 Radhika Chippada Radhika Chippada 72 Administrator can quickly reset a test user account to the "new, inactive, not invited" state with no repository/VM access, and log in to Workbench as that user, in order to efficiently test new user UI/API behavior and activation scripts. Resolved Resolved 3 1.0 1.0 1.0 2068 36 72 61 6 1.0	2482 2482 Review code updates in branch 2068-reset-user Tom, please review code updates in the branch: 2068-reset-user _(comments in #2068)_ Radhika Chippada 72 0 2068 3 36 -c-a 5 2481 2481 Invoke the API server's unsetup method from workbench when an admin user clicks on the "Deactivate" button from the user's Admin tab. Add a new link to the Admin tab. Invoke the api->unsetup mehtod when clicked. Radhika Chippada 72 0 2068 3 36 -c-a 5 2480 2480 Add functional tests for the unsetup method from the API server Radhika Chippada 72 0 2068 3 36 -c-a 5 2479 2479 Expose "unsetup" method from the API server This method deletes the login_oid_perm, repo_perm and vm_login_perm links. Also, deletes any signatures by the user. And sets the is_active to false. Add unsetup to routes, controller, and model. Radhika Chippada 72 0 2068 3 36 -c-a 5