{"__v":0,"_id":"5845ac889f79b51900b076b4","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"58458b4fba4f1c0f009692bb","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","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":[],"next":{"pages":[],"description":""},"createdAt":"2016-12-05T18:06:00.305Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"examples":{"codes":[]},"method":"post","results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":38,"body":"The example shown on this page applies specifically to TCGA. However, this page also demonstrates nested queries in the request body which is applicable to other datasets. This same nesting behavior is returned in the response body.\n\nUse the following query for TCGA if you want to see all cases which contain samples from a specific tissue source site, and you also want to know (1) the sample type code for each sample and (2) whether or not each case has a prior diagnosis.\n\n##Request\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"POST /datasets/tcga/v0/query HTTP/1.1\\nHost: cgc-datasets-api.sbgenomics.com\\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96\",\n      \"language\": \"http\",\n      \"name\": \"Find TCGA cases with or without...\"\n    }\n  ]\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n   \\\"entity\\\":\\\"cases\\\",\\n   \\\"fields\\\": [\\\"hasPriorDiagnosis\\\"],\\n   \\\"hasSample\\\" : {\\n       \\\"hasTissueSourceSiteCode\\\": \\\"ZJ\\\",\\n       \\\"fields\\\": [\\\"hasSampleTypeCode\\\"]\\n    }\\n}\",\n      \"language\": \"json\",\n      \"name\": \"Request body\"\n    }\n  ]\n}\n[/block]\nThis query specifies values for the metadata field `hasSample`. In addition, this metadata field exhibits nesting, which is possible when a metadata field refers to another entity, in this case `sample`. Recall that metadata consists of entities and their properties. These properties can either describe the entity or relate the entity to another entity. As such, the entity `hasSample` has related metadata properties, such as `hasTissueSourceSiteCode`, as is queried above. The query thus looks for cases with samples from a particular tissue source site.\n\nThis query also uses the optional key `fields` twice. `fields` exposes metadata fields to be returned by the query. For instance, the above query will return the sample type code for each sample and whether or not each case has a prior diagnosis.\n\n###Response body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"count\\\": 16,\\n  \\\"_embedded\\\": {\\n    \\\"cases\\\": [\\n      {\\n        \\\"hasPriorDiagnosis\\\": \\\"No\\\",\\n        \\\"hasSample\\\": [\\n          {\\n            \\\"id\\\": \\\"A29FDDB5-B032-43EB-A56C-A736F25596CC\\\",\\n            \\\"hasSampleTypeCode\\\": \\\"01\\\",\\n            \\\"label\\\": \\\"A29FDDB5-B032-43EB-A56C-A736F25596CC\\\",\\n            \\\"_links\\\": {\\n              \\\"self\\\": {\\n                \\\"href\\\": \\\"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/A29FDDB5-B032-43EB-A56C-A736F25596CC\\\"\\n              }\\n            }\\n          },\\n          {\\n            \\\"id\\\": \\\"1C968741-C5D4-42CE-890A-973DF7855B33\\\",\\n            \\\"hasSampleTypeCode\\\": \\\"10\\\",\\n            \\\"label\\\": \\\"1C968741-C5D4-42CE-890A-973DF7855B33\\\",\\n            \\\"_links\\\": {\\n              \\\"self\\\": {\\n                \\\"href\\\": \\\"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/1C968741-C5D4-42CE-890A-973DF7855B33\\\"\\n              }\\n            }\\n          }\\n        ],\\n        \\\"id\\\": \\\"B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\\\",\\n        \\\"label\\\": \\\"B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\\\",\\n        \\\"_links\\\": {\\n          \\\"self\\\": {\\n            \\\"href\\\": \\\"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\\\"\\n          }\\n        }\\n      },\\n \\n    < snip >\\n   ]\\n  }\\n}\",\n      \"language\": \"json\"\n    }\n  ]\n}\n[/block]\nNote that the response exhibits the same nesting as was issued in the original query. For each entity matching the query, the response contains:\n  * **Its `href`**, a path that can be used to obtain full information about the sample. In the example above, the href is located towards the end of the response (`cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`). To see all information, issue a `GET` request to this path. See [Example query 1: Find samples connected to a case](doc:example-query-1-find-samples-connected-to-a-case) for details. Note that the above response also contains `href` for each listed sample relating to the case (e.g., `cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/A29FDDB5-B032-43EB-A56C-A736F25596CC`).\n  * **Its TCGA `id`**, such as `B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`. Note that the above response also contains the `id` for each listed sample relating to the case (e.g., `A29FDDB5-B032-43EB-A56C-A736F25596CC`).\n  * **Its TCGA `label`**, such as `B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`. Note that the above response also contains the `label` for each listed sample relating to the case (e.g., `A29FDDB5-B032-43EB-A56C-A736F25596CC`).\n  * Whether or not each case has a prior diagnosis. Note that this value can be `Yes`, `No`, or `Not Available`. This exposed field does not act as a filter.\n  * The sample type code for each `sample`. Note that this value can be an integer or `Not Available`. This exposed field does not act as a filter.","excerpt":"<a href=\"query-datasets\" style=\"color:#132c56\">QUERY DATASETS</a> > <a href=\"about-the-datasets-api\" style=\"color:#132c56\">About the Datasets API</a> > <a href=\"query-via-the-datasets-api\" style=\"color:#132c56\">Query via the Datasets API</a> > Example query 6: Find TCGA cases...","slug":"example-query-6-find-tcga-cases-with-or-without-a-prior-diagnosis-and-related-samples-from-a-particular-tissue-source-site-and-return-the-sample-type-code-for-each-of-these-samples","type":"endpoint","title":"Example query 6: Find TCGA cases with or without a prior diagnosis and related samples from a particular tissue source site and return the sample type code for each of these samples"}

postExample query 6: Find TCGA cases with or without a prior diagnosis and related samples from a particular tissue source site and return the sample type code for each of these samples

<a href="query-datasets" style="color:#132c56">QUERY DATASETS</a> > <a href="about-the-datasets-api" style="color:#132c56">About the Datasets API</a> > <a href="query-via-the-datasets-api" style="color:#132c56">Query via the Datasets API</a> > Example query 6: Find TCGA cases...

The example shown on this page applies specifically to TCGA. However, this page also demonstrates nested queries in the request body which is applicable to other datasets. This same nesting behavior is returned in the response body. Use the following query for TCGA if you want to see all cases which contain samples from a specific tissue source site, and you also want to know (1) the sample type code for each sample and (2) whether or not each case has a prior diagnosis. ##Request [block:code] { "codes": [ { "code": "POST /datasets/tcga/v0/query HTTP/1.1\nHost: cgc-datasets-api.sbgenomics.com\nX-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96", "language": "http", "name": "Find TCGA cases with or without..." } ] } [/block] [block:code] { "codes": [ { "code": "{\n \"entity\":\"cases\",\n \"fields\": [\"hasPriorDiagnosis\"],\n \"hasSample\" : {\n \"hasTissueSourceSiteCode\": \"ZJ\",\n \"fields\": [\"hasSampleTypeCode\"]\n }\n}", "language": "json", "name": "Request body" } ] } [/block] This query specifies values for the metadata field `hasSample`. In addition, this metadata field exhibits nesting, which is possible when a metadata field refers to another entity, in this case `sample`. Recall that metadata consists of entities and their properties. These properties can either describe the entity or relate the entity to another entity. As such, the entity `hasSample` has related metadata properties, such as `hasTissueSourceSiteCode`, as is queried above. The query thus looks for cases with samples from a particular tissue source site. This query also uses the optional key `fields` twice. `fields` exposes metadata fields to be returned by the query. For instance, the above query will return the sample type code for each sample and whether or not each case has a prior diagnosis. ###Response body [block:code] { "codes": [ { "code": "{\n \"count\": 16,\n \"_embedded\": {\n \"cases\": [\n {\n \"hasPriorDiagnosis\": \"No\",\n \"hasSample\": [\n {\n \"id\": \"A29FDDB5-B032-43EB-A56C-A736F25596CC\",\n \"hasSampleTypeCode\": \"01\",\n \"label\": \"A29FDDB5-B032-43EB-A56C-A736F25596CC\",\n \"_links\": {\n \"self\": {\n \"href\": \"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/A29FDDB5-B032-43EB-A56C-A736F25596CC\"\n }\n }\n },\n {\n \"id\": \"1C968741-C5D4-42CE-890A-973DF7855B33\",\n \"hasSampleTypeCode\": \"10\",\n \"label\": \"1C968741-C5D4-42CE-890A-973DF7855B33\",\n \"_links\": {\n \"self\": {\n \"href\": \"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/1C968741-C5D4-42CE-890A-973DF7855B33\"\n }\n }\n }\n ],\n \"id\": \"B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\",\n \"label\": \"B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\",\n \"_links\": {\n \"self\": {\n \"href\": \"cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9\"\n }\n }\n },\n \n < snip >\n ]\n }\n}", "language": "json" } ] } [/block] Note that the response exhibits the same nesting as was issued in the original query. For each entity matching the query, the response contains: * **Its `href`**, a path that can be used to obtain full information about the sample. In the example above, the href is located towards the end of the response (`cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`). To see all information, issue a `GET` request to this path. See [Example query 1: Find samples connected to a case](doc:example-query-1-find-samples-connected-to-a-case) for details. Note that the above response also contains `href` for each listed sample relating to the case (e.g., `cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/A29FDDB5-B032-43EB-A56C-A736F25596CC`). * **Its TCGA `id`**, such as `B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`. Note that the above response also contains the `id` for each listed sample relating to the case (e.g., `A29FDDB5-B032-43EB-A56C-A736F25596CC`). * **Its TCGA `label`**, such as `B12DEB95-6AA1-49CB-A3C5-A711D42D6FB9`. Note that the above response also contains the `label` for each listed sample relating to the case (e.g., `A29FDDB5-B032-43EB-A56C-A736F25596CC`). * Whether or not each case has a prior diagnosis. Note that this value can be `Yes`, `No`, or `Not Available`. This exposed field does not act as a filter. * The sample type code for each `sample`. Note that this value can be an integer or `Not Available`. This exposed field does not act as a filter.