{"action":"created","issue":{"url":"https://api.github.com/repos/terraref/computing-pipeline/issues/33","repository_url":"https://api.github.com/repos/terraref/computing-pipeline","labels_url":"https://api.github.com/repos/terraref/computing-pipeline/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/terraref/computing-pipeline/issues/33/comments","events_url":"https://api.github.com/repos/terraref/computing-pipeline/issues/33/events","html_url":"https://github.com/terraref/computing-pipeline/issues/33","id":117430509,"number":33,"title":"Insert derived traits and meta-data from PlantCV pipeline into BETYdb","user":{"login":"dlebauer","id":464871,"avatar_url":"https://avatars.githubusercontent.com/u/464871?v=3","gravatar_id":"","url":"https://api.github.com/users/dlebauer","html_url":"https://github.com/dlebauer","followers_url":"https://api.github.com/users/dlebauer/followers","following_url":"https://api.github.com/users/dlebauer/following{/other_user}","gists_url":"https://api.github.com/users/dlebauer/gists{/gist_id}","starred_url":"https://api.github.com/users/dlebauer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dlebauer/subscriptions","organizations_url":"https://api.github.com/users/dlebauer/orgs","repos_url":"https://api.github.com/users/dlebauer/repos","events_url":"https://api.github.com/users/dlebauer/events{/privacy}","received_events_url":"https://api.github.com/users/dlebauer/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/terraref/computing-pipeline/labels/1%20-%20Ready","name":"1 - Ready","color":"CCCCCC"}],"state":"open","locked":false,"assignee":{"login":"nfahlgren","id":6233508,"avatar_url":"https://avatars.githubusercontent.com/u/6233508?v=3","gravatar_id":"","url":"https://api.github.com/users/nfahlgren","html_url":"https://github.com/nfahlgren","followers_url":"https://api.github.com/users/nfahlgren/followers","following_url":"https://api.github.com/users/nfahlgren/following{/other_user}","gists_url":"https://api.github.com/users/nfahlgren/gists{/gist_id}","starred_url":"https://api.github.com/users/nfahlgren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nfahlgren/subscriptions","organizations_url":"https://api.github.com/users/nfahlgren/orgs","repos_url":"https://api.github.com/users/nfahlgren/repos","events_url":"https://api.github.com/users/nfahlgren/events{/privacy}","received_events_url":"https://api.github.com/users/nfahlgren/received_events","type":"User","site_admin":false},"assignees":[{"login":"nfahlgren","id":6233508,"avatar_url":"https://avatars.githubusercontent.com/u/6233508?v=3","gravatar_id":"","url":"https://api.github.com/users/nfahlgren","html_url":"https://github.com/nfahlgren","followers_url":"https://api.github.com/users/nfahlgren/followers","following_url":"https://api.github.com/users/nfahlgren/following{/other_user}","gists_url":"https://api.github.com/users/nfahlgren/gists{/gist_id}","starred_url":"https://api.github.com/users/nfahlgren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nfahlgren/subscriptions","organizations_url":"https://api.github.com/users/nfahlgren/orgs","repos_url":"https://api.github.com/users/nfahlgren/repos","events_url":"https://api.github.com/users/nfahlgren/events{/privacy}","received_events_url":"https://api.github.com/users/nfahlgren/received_events","type":"User","site_admin":false}],"milestone":null,"comments":13,"created_at":"2015-11-17T19:29:12Z","updated_at":"2016-07-05T21:32:05Z","closed_at":null,"body":"After phenotypes are extracted from PlantCV pipeline, plant-level traits should be inserted into BETYdb, Traits described in [Fahlgren et al 2015](https://github.com/terraref/computing-pipeline/files/37098/fahlgren_et_al_2015.pdf).\r\n\r\n## Meta-data:\r\n\r\n* genotype --> cultivars table; traits.cultivar_id\r\n* date / time --> traits.date traits.time\r\n* site --> Danforth Lemnatec System\r\n* method: PlantCV (sensor name, version)\r\n\r\n## Data (traits):\r\n\r\n* Fv/Fm\r\n* height\r\n* shoot + leaf area\r\n* water use efficiency\r\n* Absolute growth rate\r\n* Fresh-weight biomass\r\n* height:width ratio\r\n* tiller count\r\n\r\n<!---\r\n@huboard:{\"order\":8.25,\"milestone_order\":33,\"custom_state\":\"\"}\n-->\r\n"},"comment":{"url":"https://api.github.com/repos/terraref/computing-pipeline/issues/comments/230609426","html_url":"https://github.com/terraref/computing-pipeline/issues/33#issuecomment-230609426","issue_url":"https://api.github.com/repos/terraref/computing-pipeline/issues/33","id":230609426,"user":{"login":"nfahlgren","id":6233508,"avatar_url":"https://avatars.githubusercontent.com/u/6233508?v=3","gravatar_id":"","url":"https://api.github.com/users/nfahlgren","html_url":"https://github.com/nfahlgren","followers_url":"https://api.github.com/users/nfahlgren/followers","following_url":"https://api.github.com/users/nfahlgren/following{/other_user}","gists_url":"https://api.github.com/users/nfahlgren/gists{/gist_id}","starred_url":"https://api.github.com/users/nfahlgren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nfahlgren/subscriptions","organizations_url":"https://api.github.com/users/nfahlgren/orgs","repos_url":"https://api.github.com/users/nfahlgren/repos","events_url":"https://api.github.com/users/nfahlgren/events{/privacy}","received_events_url":"https://api.github.com/users/nfahlgren/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T21:32:05Z","updated_at":"2016-07-05T21:32:05Z","body":"@dlebauer I signed up for a BETYdb account. The information you added looks good. I will have to check on the additional information about the sorghum varieties used in the pilot.\r\n\r\n@gsrohde you are correct about plant_barcode, we don't need it in the database (redundant with cultivar and treatment). For the column mappings above (e.g. genotype => cultivar), do we need to change the nomenclature in Clowder or is this just how they are being mapped? Happy to change it on the Clowder end.\r\n\r\n@gsrohde the current imagedate is in local_datetime, so we would need to add the timezone information to the Danforth Center site entry. If UTC is preferred I can have the extractor convert it."}}
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