{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/259","repository_url":"https://api.github.com/repos/PacificBiosciences/smrtflow","labels_url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/259/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/259/comments","events_url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/259/events","html_url":"https://github.com/PacificBiosciences/smrtflow/pull/259","id":167712142,"number":259,"title":"smrt-server-lims code. Ready for code review","user":{"login":"jfalkner","id":855834,"avatar_url":"https://avatars.githubusercontent.com/u/855834?v=3","gravatar_id":"","url":"https://api.github.com/users/jfalkner","html_url":"https://github.com/jfalkner","followers_url":"https://api.github.com/users/jfalkner/followers","following_url":"https://api.github.com/users/jfalkner/following{/other_user}","gists_url":"https://api.github.com/users/jfalkner/gists{/gist_id}","starred_url":"https://api.github.com/users/jfalkner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jfalkner/subscriptions","organizations_url":"https://api.github.com/users/jfalkner/orgs","repos_url":"https://api.github.com/users/jfalkner/repos","events_url":"https://api.github.com/users/jfalkner/events{/privacy}","received_events_url":"https://api.github.com/users/jfalkner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"assignees":[{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false}],"milestone":null,"comments":20,"created_at":"2016-07-26T21:07:38Z","updated_at":"2016-08-08T16:17:45Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/PacificBiosciences/smrtflow/pulls/259","html_url":"https://github.com/PacificBiosciences/smrtflow/pull/259","diff_url":"https://github.com/PacificBiosciences/smrtflow/pull/259.diff","patch_url":"https://github.com/PacificBiosciences/smrtflow/pull/259.patch"},"body":"CC @mpkocher \r\n\r\nThis is a rebase of all the smrt-sever-lims server-side code in its current state. Pair this with [jfalkner/SmrtLimsUI](https://github.com/jfalkner/SmrtLimsUI) for example client-side code in HTML/CSS/JS + ReactJS.\r\n\r\nSee the [README.md](https://github.com/PacificBiosciences/smrtflow/blob/77406002fbe657d87c6a77683ceeec2c8d42809a/smrt-server-lims/README.md) for how to run, test, example use cases and link to the drafted [specification.md](https://github.com/PacificBiosciences/smrtflow/blob/77406002fbe657d87c6a77683ceeec2c8d42809a/smrt-server-lims/README.md). The `./scripts` dir has helper scripts that use `find` and `curl` to scan for all PacBio `lims.yml` files and import them to the service -- the main use case tested.\r\n\r\nThe core web services are exercised by two tests (as noted in [README.md](https://github.com/PacificBiosciences/smrtflow/blob/77406002fbe657d87c6a77683ceeec2c8d42809a/smrt-server-lims/README.md#tests)). [RouteImportAndResolveSpec]() exercises the API in a linear fashion and is a good bit of code to read first.\r\n\r\n## UI Example\r\n\r\nHere is an example of the UI that is using this PR's code as the server-side backing. Very similar to the old UI that relied on ES. The UI is easy to update but not part of an official build.\r\n\r\n<img width=\"1094\" alt=\"screen shot 2016-07-25 at 1 34 31 pm\" src=\"https://cloud.githubusercontent.com/assets/855834/17155268/5c4b9224-5352-11e6-97b5-74b77905005a.png\">\r\n\r\nIn order to replicate the above, host the static web UI straight from the repo.\r\n\r\n```bash\r\n# Host this checkout as a website\r\ngit clone https://github.com/jfalkner/SmrtLimsUI.git\r\ncd SmrtLimsUI\r\npython -m SimpleHTTPServer\r\n```\r\n\r\nIn a different terminal, checkout and run the server-side code.\r\n\r\n```bash\r\ngit clone <this_repo>\r\nsbt clean compile smrt-server-lims/run\r\n# could also use `sbt smrt-server-lims/assembly` then run the JAR \r\n```\r\n\r\nNow the server should be available on `http://127.0.0.1:8070`. Use curl to copy over data from `/pbi/collections`.\r\n\r\n```\r\n# use curl via helper script. see script for details\r\ncd smrt-server-lims/scripts\r\n./import_lims_.sh /pbi/collections/312/3120145/r54009_20160426_164705/1_A01/lims.yml\r\n```\r\n\r\nNow visit the same URL as in the screenshot: `http://localhost:63342/SmrtLimsUI/index.html?q=3120145`"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/comments/238288715","html_url":"https://github.com/PacificBiosciences/smrtflow/pull/259#issuecomment-238288715","issue_url":"https://api.github.com/repos/PacificBiosciences/smrtflow/issues/259","id":238288715,"user":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"created_at":"2016-08-08T16:17:45Z","updated_at":"2016-08-08T16:17:45Z","body":"I'm seeing errors, but the failures look different than the failures in Circle.\r\n\r\n```\r\n[info] x API should fail pre-import: lookup via expcode\r\n[error]    '1' is not equal to '0' (CommandLineToolsSpec.scala:76)\r\n[info] \r\n[info] x CLI should fail pre-import: get-expcode\r\n[error]    ''\r\n[error]    \r\n[error]     is not equal to \r\n[error]    \r\n[error]    'Failed to run spray.httpx.UnsuccessfulResponseException: Status: 404 Not Found\r\n[error]    Body: []\r\n[error]    ' (CommandLineToolsSpec.scala:78)\r\n[error] Expected: Failed to run spray.httpx.UnsuccessfulResponseException: Status: 404 Not Found\r\n[error] Body: []\r\n[error] Actual:   \r\n[info] \r\n[info] + API should fail pre-import: lookup via runcode\r\n[info] + CLI should fail pre-import: get-runcode\r\n[info] + Import data from POST\r\n[info] + API lookup via expcode works\r\n[info] x CLI get-expcode works\r\n[error]    'List(LimsSubreadSet(8fed57d4-5233-4836-8c86-c005a2a5b711,3220001,3220001-0001,/tmp/mutli_import_and_results6803353945513953758/3220001-0001,3.0.17,3.0.5.175014,A01,m54009_160426_165001,2016-04-26T18:46:06Z,Inst54009,54009), LimsSubreadSet(5fe01e82-c694-4575-9173-c23c458dd0e1,3220001,3220001-0006,/tmp/CLI6380546418444418383,3.0.17,3.0.5.175014,A01,m54009_160426_165001,2016-04-26T18:46:06Z,Inst54009,54009))\r\n[error]    '\r\n[error]    \r\n[error]     is not equal to \r\n[error]    \r\n[error]    'List(LimsSubreadSet(5fe01e82-c694-4575-9173-c23c458dd0e1,3220001,3220001-0006,/tmp/CLI6380546418444418383,3.0.17,3.0.5.175014,A01,m54009_160426_165001,2016-04-26T18:46:06Z,Inst54009,54009))\r\n[error]    ' (CommandLineToolsSpec.scala:92)\r\n[error] Expected: ...dSet([5]fe[01e82]-[c694]-4[575]-[9173]-c[23c458dd0e]1,...00[6],/...p/[CLI63]80[]5[]4[64]1[]8[4444]1[8383],3...:4[6:06Z,Inst54009,54009))]\r\n[error] Actual:   ...dSet([8]fe[d57d4]-[5233]-4[836]-[8c86]-c[005a2a5b71]1,...00[1],/...p/[mutli_import_and_results6]80[33]5[39]4[55]1[395375]8[/322000]1[-0001],3...:4[]\r\n[info] \r\n[info] + API lookup via runcode works\r\n[info] + CLI get-expcode works\r\n[info] + API lookup via UUID works\r\n[info] + CLI get-uuid works\r\n[info] \r\n[info] Total for specification CommandLineToolsSpec\r\n[info] Finished in 327 ms\r\n[info] 11 examples, 3 failures, 0 error\r\n[error] Failed: Total 29, Failed 3, Errors 0, Passed 26\r\n[error] Failed tests:\r\n[error] \tcom.pacbio.secondary.lims.CommandLineToolsSpec\r\n[error] (smrt-server-lims/test:test) sbt.TestsFailedException: Tests unsuccessful\r\n[error] Total time: 335 s, completed Aug 8, 2016 8:57:18 AM\r\n```"}}
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