{"__v":4,"_id":"569557e2fcb1032d0089dfe2","category":{"__v":92,"_id":"55faf9aa17b9d00d00969f49","pages":["56312d239ead230d00a188f2","56312e0d82d96a0d00b0fb08","56315777fc94aa0d00e9b553","56315b779ead230d00a1894a","5631657c9c25801700dac34f","56317884fc94aa0d00e9b586","56318386c3b04b0d00ba9bb9","563240ccdcc27a170082363b","563240dfbddb091700ad5e82","563240edfe9acd1900cc1d10","56324504fa40240d007c8d5f","56324b30c3b04b0d00ba9c96","563273ae45f2cb0d006be3fa","563273c08c9cda0d0025266d","563273cc38f8aa0d00d30f55","563273d838f8aa0d00d30f59","5632740945f2cb0d006be3fc","56327411df556c0d00cd0905","5632741b8c9cda0d0025266f","563274ea10b6040d008793d8","5632757cdf556c0d00cd0908","563275b710b6040d008793da","563275f938f8aa0d00d30f60","5632762fb904a10d0032f6fc","5632767110b6040d008793dd","563276c0b904a10d0032f700","5632770162c48a0d00334d53","5632843d8c9cda0d00252698","5632846e62c48a0d00334d78","56328a7e49e16d0d00122420","56328aaf49e16d0d00122425","56328b2238f8aa0d00d30f88","56328b6c8c9cda0d002526a2","56328c0710b6040d008793ff","56328c3710b6040d00879401","56328c5938f8aa0d00d30f8c","56328c90b904a10d0032f722","56328cc449e16d0d0012242a","56328ce68c9cda0d002526a8","56328d1338f8aa0d00d30f8e","56328d5810b6040d00879407","56328d7cdf556c0d00cd092f","56328d9a10b6040d00879409","56328db438f8aa0d00d30f92","56328dd762c48a0d00334d8b","56328df649e16d0d0012242d","56328e1edf556c0d00cd0931","56328e4662c48a0d00334d8e","56328e5edf556c0d00cd0933","56328e8f8c9cda0d002526ab","56328eb3b904a10d0032f72a","56328edb38f8aa0d00d30f95","56328ef210b6040d0087940d","56328f148c9cda0d002526ad","56328f2962c48a0d00334d90","56328f54b904a10d0032f72c","56328f6c38f8aa0d00d30f98","56328f858c9cda0d002526af","56328fae62c48a0d00334d95","56328fd838f8aa0d00d30f9c","5637f069ee0ee60d0024ec18","5641ffaa9417b40d00c0fc35","564355240d9748190079dea9","5644cfeb2c74cf1900da4831","56450f856b0ca50d00f6bd8f","56706537cbb2fb0d00f7c7dd","567065bc3d29830d00376213","56706fc2cbb2fb0d00f7c87e","568bf5a1e662f40d00eee866","568c0699e662f40d00eee881","568cff0274c77f2d00d56d51","568d10f58602880d001ce277","568d2abc37b636250036b904","568d343413c5ad0d00b34efb","568d593a8602880d001ce2d3","568e64135e12fb0d00325160","568e66f05e12fb0d00325162","568e78aa5e12fb0d0032517a","569433cfd8c04d1700e5ae0c","56943723d8c04d1700e5ae14","5694393b3e9d080d00f0655d","5694e6cf953b810d008f91bc","5694f301c5c5ce0d00058e68","569502ef9797fa1900f704e7","5695063bcaa32519009c40b3","569511cccaa32519009c40d9","569557e2fcb1032d0089dfe2","569562fefcb1032d0089dfee","56956428fe18811700c9c058","569639b87596a90d0014e5a3","56a90197e590350d004b5103","56a9021e9ec7660d002e08c2"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":true,"createdAt":"2015-09-17T17:34:34.937Z","from_sync":false,"order":26,"slug":"api","title":"API Reference"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"554340dfb7f4540d00fcef1d","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":["56a734182ec8310d007bc2b7"],"next":{"pages":[],"description":""},"createdAt":"2016-01-12T19:45:38.910Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[]},"method":"patch","results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":true,"order":73,"body":"This call allows you to change the details of the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](doc:list-tasks-you-can-access).\n\nYou can change a task's name, description, and inputs.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"title\": \"Specifying task inputs\",\n  \"body\": \"See the section on [inputs](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-inputs) in the [API Overview](doc:the-cgc-api) for details on how to refer to a task's inputs.\"\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"title\": \"Modifying tasks\",\n  \"body\": \"Note that you can only modify tasks with the [status](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-tasks) `DRAFT`, not those with statuses `RUNNING`, `QUEUED`, `ABORTED`, `COMPLETED` or `FAILED`. This feature is to enable reproducibility of any analysis that has been queued for execution or has initiated executing.\"\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"https://cgc-api.sbgenomics.com/v2/tasks/{task_id}\",\n      \"language\": \"text\",\n      \"name\": \"Path\"\n    }\n  ]\n}\n[/block]\n##Request\n\n###Example request\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"PATCH /v2/tasks/08c5ce64-1551-4b7d-b054-63a1517bc7bb HTTP/1.1\\nHost: cgc-api.sbgenomics.com\\nX-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74\\n\",\n      \"language\": \"http\",\n      \"name\": null\n    },\n    {\n      \"code\": \"curl  --data-binary \\\":::at:::modify-task.json\\\" -s -H \\\"X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7\\\" -H \\\"content-type: application/json\\\" -X PATCH \\\"https://cgc-api.sbgenomics.com/v2/tasks/08c5ce64-1551-4b7d-b054-63a1517bc7bb\\\"\",\n      \"language\": \"curl\",\n      \"name\": \"cURL\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\nSee below for an example of the content of the request, sent here as `modify-task.json`.\n\n###Header Fields\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"`X-SBG-Auth-Token`\\n_required_\",\n    \"0-1\": \"Your CGC [authentication token](doc:get-your-authentication-token).\",\n    \"h-2\": \"\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n###Path parameters\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"`task_id`\\n_required_\",\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"The ID of the task you are querying\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n###Query parameters\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Data type\",\n    \"h-2\": \"Description\",\n    \"0-0\": \"`fields`\",\n    \"0-1\": \"string\",\n    \"0-2\": \"Selector specifying a subset of fields to include in the response.\"\n  },\n  \"cols\": 3,\n  \"rows\": 1\n}\n[/block]\n##Request body\nIn the body of the request you should enter key-value pairs, as explained below:\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Key\",\n    \"h-1\": \"Datatype of value\",\n    \"h-2\": \"Description of value\",\n    \"0-0\": \"`\\\"name\\\"`\",\n    \"1-0\": \"`\\\"description\\\"`\",\n    \"2-0\": \"`\\\"inputs\\\"`\",\n    \"0-1\": \"string\",\n    \"1-1\": \"string\",\n    \"2-1\": \"dictionary\",\n    \"0-2\": \"The name of the task\",\n    \"1-2\": \"The description of the task\",\n    \"2-2\": \"See the [API Overview](doc:the-cgc-api)  section on [specifying inputs](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-inputs) for information on creating input objects.\",\n    \"3-0\": \"`\\\"batch_input\\\"`\",\n    \"4-0\": \"`\\\"batch_by\\\"`\",\n    \"3-1\": \"string\",\n    \"4-1\": \"dictionary\",\n    \"3-2\": \"The ID of the input on which you wish to batch. You would typically batch on the input consisting of a list of files. If this parameter is omitted, the default batching criteria defined for the app will be used.\",\n    \"4-2\": \"This specifies the criteria on which to batch. It can be in one of two formats.\\n\\n1. If you wish to batch per item in the app's input (i.e., typically per file in a list of files) then specify a dictionary with the following format:\\n`{\\n   \\\"type\\\": \\\"ITEM\\\"\\n}`\\n\\n2. If you wish to batch by groups of inputs, you should specify the criteria satisfied by each group. This should be a common metadata value in one, or more, metadata fields.\\n\\nTo do this, specify a dictionary with the following format:\\n\\n`{\\n   \\\"type\\\": \\\"CRITERIA\\\",\\n   \\\"criteria\\\": [\\n        \\\"metadata.<field_1>\\\", \\\"metadata.<field_2>\\\"\\n    ]\\n}`\\nThis will group inputs by shared metadata values for `<field_1>` and `<field_2>`, in that order. Arbitrarily many metadata fields may be listed, and the order in which fields are grouped will respect the order of the list.\"\n  },\n  \"cols\": 3,\n  \"rows\": 5\n}\n[/block]\nThere are two further things to note if you are editing a batch task:\n\nIf you want to change the input on which to batch and the batch criteria, you need to specify the `batch_input` and `batch_by` parameters together in the same PATCH request.\n\nIf you want to disable batching on a task, set the parameters `batch_input` and `batch_by` to the JSON null value, as follows:\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n    \\\"batch_input\\\": null,\\n    \\\"batch_by\\\" : null    \\n}\",\n      \"language\": \"json\"\n    }\n  ]\n}\n[/block]\n###Example request body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"name\\\": \\\"new name for my task\\\",\\n  \\\"description\\\": \\\"re-describing the task\\\",\\n  \\\"inputs\\\": {\\n\\n        \\\"cuffdiff_zip\\\": {\\n            \\\"class\\\": \\\"File\\\",\\n            \\\"path\\\": \\\"562785e6e4b00a1d67a8b1aa\\\",\\n            \\\"name\\\": \\\"example_human_known_indels.vcf\\\"\\n        }\\n}\",\n      \"language\": \"json\"\n    }\n  ]\n}\n[/block]\n##Response\n[See a list of CGC-specific response codes that may be contained in the body of the response.](doc:api-status-codes) \n\n###Example response body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"href\\\": \\\"https://cgc-api.sbgenomics.com/v2/tasks/234edb2d-a866-4828-a7c3-0aa757f991e7\\\",\\n  \\\"id\\\": \\\"234edb2d-a866-4828-a7c3-0aa757f991e7\\\",\\n  \\\"name\\\": \\\"new name for my task\\\",\\n  \\\"description\\\": \\\"re-describing the task\\\",\\n  \\\"status\\\": \\\"DRAFT\\\",\\n  \\\"project\\\": \\\"RFranklin/my-project\\\",\\n  \\\"app\\\": \\\"RFranklin/my-project/new/0\\\",\\n  \\\"type\\\": \\\"v2\\\",\\n  \\\"created_by\\\": \\\"RFranklin\\\",\\n  \\\"start_time\\\": \\\"2016-01-12T18:39:30Z\\\",\\n  \\\"inputs\\\": {\\n    \\\"dispersion_threshold\\\": null,\\n    \\\"cuffdiff_zip\\\": {\\n      \\\"class\\\": \\\"File\\\",\\n      \\\"path\\\": \\\"562785e6e4b00a1d67a8b1aa\\\",\\n      \\\"name\\\": \\\"example_human_known_indels.vcf\\\"\\n    },\\n    \\\"density_threshold\\\": null,\\n    \\\"thresholds_off\\\": null\\n  },\\n  \\\"outputs\\\": {\\n    \\\"archive\\\": null,\\n    \\\"html\\\": null\\n  }\\n}\\n\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]","excerpt":"/tasks/{task_id}","slug":"modify-a-task","type":"endpoint","title":"Modify a task"}

patchModify a task

/tasks/{task_id}

This call allows you to change the details of the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](doc:list-tasks-you-can-access). You can change a task's name, description, and inputs. [block:callout] { "type": "success", "title": "Specifying task inputs", "body": "See the section on [inputs](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-inputs) in the [API Overview](doc:the-cgc-api) for details on how to refer to a task's inputs." } [/block] [block:callout] { "type": "success", "title": "Modifying tasks", "body": "Note that you can only modify tasks with the [status](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-tasks) `DRAFT`, not those with statuses `RUNNING`, `QUEUED`, `ABORTED`, `COMPLETED` or `FAILED`. This feature is to enable reproducibility of any analysis that has been queued for execution or has initiated executing." } [/block] [block:code] { "codes": [ { "code": "https://cgc-api.sbgenomics.com/v2/tasks/{task_id}", "language": "text", "name": "Path" } ] } [/block] ##Request ###Example request [block:code] { "codes": [ { "code": "PATCH /v2/tasks/08c5ce64-1551-4b7d-b054-63a1517bc7bb HTTP/1.1\nHost: cgc-api.sbgenomics.com\nX-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74\n", "language": "http", "name": null }, { "code": "curl --data-binary \"@modify-task.json\" -s -H \"X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7\" -H \"content-type: application/json\" -X PATCH \"https://cgc-api.sbgenomics.com/v2/tasks/08c5ce64-1551-4b7d-b054-63a1517bc7bb\"", "language": "curl", "name": "cURL" } ], "sidebar": true } [/block] See below for an example of the content of the request, sent here as `modify-task.json`. ###Header Fields [block:parameters] { "data": { "h-0": "Name", "h-1": "Description", "0-0": "`X-SBG-Auth-Token`\n_required_", "0-1": "Your CGC [authentication token](doc:get-your-authentication-token).", "h-2": "" }, "cols": 2, "rows": 1 } [/block] ###Path parameters [block:parameters] { "data": { "0-0": "`task_id`\n_required_", "h-0": "Name", "h-1": "Description", "0-1": "The ID of the task you are querying" }, "cols": 2, "rows": 1 } [/block] ###Query parameters [block:parameters] { "data": { "h-0": "Name", "h-1": "Data type", "h-2": "Description", "0-0": "`fields`", "0-1": "string", "0-2": "Selector specifying a subset of fields to include in the response." }, "cols": 3, "rows": 1 } [/block] ##Request body In the body of the request you should enter key-value pairs, as explained below: [block:parameters] { "data": { "h-0": "Key", "h-1": "Datatype of value", "h-2": "Description of value", "0-0": "`\"name\"`", "1-0": "`\"description\"`", "2-0": "`\"inputs\"`", "0-1": "string", "1-1": "string", "2-1": "dictionary", "0-2": "The name of the task", "1-2": "The description of the task", "2-2": "See the [API Overview](doc:the-cgc-api) section on [specifying inputs](http://docs.cancergenomicscloud.org/v1.0/docs/the-cgc-api#section-inputs) for information on creating input objects.", "3-0": "`\"batch_input\"`", "4-0": "`\"batch_by\"`", "3-1": "string", "4-1": "dictionary", "3-2": "The ID of the input on which you wish to batch. You would typically batch on the input consisting of a list of files. If this parameter is omitted, the default batching criteria defined for the app will be used.", "4-2": "This specifies the criteria on which to batch. It can be in one of two formats.\n\n1. If you wish to batch per item in the app's input (i.e., typically per file in a list of files) then specify a dictionary with the following format:\n`{\n \"type\": \"ITEM\"\n}`\n\n2. If you wish to batch by groups of inputs, you should specify the criteria satisfied by each group. This should be a common metadata value in one, or more, metadata fields.\n\nTo do this, specify a dictionary with the following format:\n\n`{\n \"type\": \"CRITERIA\",\n \"criteria\": [\n \"metadata.<field_1>\", \"metadata.<field_2>\"\n ]\n}`\nThis will group inputs by shared metadata values for `<field_1>` and `<field_2>`, in that order. Arbitrarily many metadata fields may be listed, and the order in which fields are grouped will respect the order of the list." }, "cols": 3, "rows": 5 } [/block] There are two further things to note if you are editing a batch task: If you want to change the input on which to batch and the batch criteria, you need to specify the `batch_input` and `batch_by` parameters together in the same PATCH request. If you want to disable batching on a task, set the parameters `batch_input` and `batch_by` to the JSON null value, as follows: [block:code] { "codes": [ { "code": "{\n \"batch_input\": null,\n \"batch_by\" : null \n}", "language": "json" } ] } [/block] ###Example request body [block:code] { "codes": [ { "code": "{\n \"name\": \"new name for my task\",\n \"description\": \"re-describing the task\",\n \"inputs\": {\n\n \"cuffdiff_zip\": {\n \"class\": \"File\",\n \"path\": \"562785e6e4b00a1d67a8b1aa\",\n \"name\": \"example_human_known_indels.vcf\"\n }\n}", "language": "json" } ] } [/block] ##Response [See a list of CGC-specific response codes that may be contained in the body of the response.](doc:api-status-codes) ###Example response body [block:code] { "codes": [ { "code": "{\n \"href\": \"https://cgc-api.sbgenomics.com/v2/tasks/234edb2d-a866-4828-a7c3-0aa757f991e7\",\n \"id\": \"234edb2d-a866-4828-a7c3-0aa757f991e7\",\n \"name\": \"new name for my task\",\n \"description\": \"re-describing the task\",\n \"status\": \"DRAFT\",\n \"project\": \"RFranklin/my-project\",\n \"app\": \"RFranklin/my-project/new/0\",\n \"type\": \"v2\",\n \"created_by\": \"RFranklin\",\n \"start_time\": \"2016-01-12T18:39:30Z\",\n \"inputs\": {\n \"dispersion_threshold\": null,\n \"cuffdiff_zip\": {\n \"class\": \"File\",\n \"path\": \"562785e6e4b00a1d67a8b1aa\",\n \"name\": \"example_human_known_indels.vcf\"\n },\n \"density_threshold\": null,\n \"thresholds_off\": null\n },\n \"outputs\": {\n \"archive\": null,\n \"html\": null\n }\n}\n", "language": "json" } ], "sidebar": true } [/block]