{"action":"opened","issue":{"url":"https://api.github.com/repos/cfe-lab/MiCall/issues/358","repository_url":"https://api.github.com/repos/cfe-lab/MiCall","labels_url":"https://api.github.com/repos/cfe-lab/MiCall/issues/358/labels{/name}","comments_url":"https://api.github.com/repos/cfe-lab/MiCall/issues/358/comments","events_url":"https://api.github.com/repos/cfe-lab/MiCall/issues/358/events","html_url":"https://github.com/cfe-lab/MiCall/issues/358","id":177227535,"number":358,"title":"Try retrieving run data from samples without making the user provide it","user":{"login":"donkirkby","id":1639148,"avatar_url":"https://avatars.githubusercontent.com/u/1639148?v=3","gravatar_id":"","url":"https://api.github.com/users/donkirkby","html_url":"https://github.com/donkirkby","followers_url":"https://api.github.com/users/donkirkby/followers","following_url":"https://api.github.com/users/donkirkby/following{/other_user}","gists_url":"https://api.github.com/users/donkirkby/gists{/gist_id}","starred_url":"https://api.github.com/users/donkirkby/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/donkirkby/subscriptions","organizations_url":"https://api.github.com/users/donkirkby/orgs","repos_url":"https://api.github.com/users/donkirkby/repos","events_url":"https://api.github.com/users/donkirkby/events{/privacy}","received_events_url":"https://api.github.com/users/donkirkby/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-09-15T16:43:22Z","updated_at":"2016-09-15T16:43:22Z","closed_at":null,"body":"In a [discussion][] in the BaseSpace forum, I learned that you can access the BaseSpace API using the access token from the `$AccessToken` environment variable. That means we should be able to just accept a list of samples, and find the run data for each sample through calls to the API. The chain I followed was:\r\n\r\n* [Sample][] - includes a set of [Properties][], one of which is the run this sample came from\r\n* [Run][] - gets the details of a run, but you can probably skip that, and go directly to the files\r\n* [Run files][] - lists the files associated with a run, but there are a ton of them. Using the `Extensions` filter to list `.bin` files works fine, though.\r\n* [File content][] - downloads the contents of a file\r\n\r\n[discussion]: https://groups.google.com/d/msg/basespace-developers/HSQGGzRMO34/WtCdUSs0FgAJ\r\n[Sample]: https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference#Samples\r\n[Properties]: https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference#Properties\r\n[Runs]: https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference#Runs\r\n[Run files]: https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference#GETrunsidfiles\r\n[File content]: https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference#GETfilesIdcontent"}}
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